Fianna Fáil has ratified the Programme for Government at a special Ard Fheis in Dublin.
812 members voted in favour of going back into Government to 62 against.
The Fianna Fáil leader hit out at the negativity in some quarters around the formation of the incoming government.
Speaking after his party ratified the Programme for Government, Mr Martin insisted that Independent TD Michael Lowry was "not in" the new government.
He praised the work of the Moriarty Tribunal, which made findings against Mr Lowry, saying what the tribunal revealed was shocking and wrong.
However, he said that he had confidence in Mr Lowry's ability to negotiate on behalf of the Regional Independents after Labour and the Social Democrats were not "disposed to going into government".
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Mr Martin said he was determined to form a government and while he does not in any way condone what emerged from the Moriarty Tribunal, the people of Tipperary have elected Mr Lowry and that cannot be ignored.
Earlier, he hit out at who he called the "naysayers" who he believes do not like the look of the new government.
Amid accusations that the Regional Independent TDs are hijacking opposition time by opting to sit away from the government in the Dáil, Mr Martin contended that this was not issue which was exercising the public.
He pledged that the coalition comprising of his party, Fine Gael and the Regional Independents would address disability issues once and for all.
There was a promise too that the pro-enterprise economy would be protected and housing would remain the top priority.
Mr Martin is set to be elected Taoiseach on Wednesday, and he is in line to hold that role until the middle of November 2027 when the position would rotate to Fine Gael Leader Simon Harris.
While Fianna Fáil organised a one-off conference to rubber-stamp the Programme for Government, Fine Gael is holding a series of five regional meetings, the last two of which will take place in Meath and Cork this afternoon.
The results of the secret ballots held at the Fine Gael meetings will be announced tomorrow.
Canney raised question of additional expenses for junior ministers
Independent TD Seán Canney has confirmed that he raised the question of additional expenses for junior ministers during the Programme for Government negotiations.
It is expected that junior ministers appointed to the new government on Wednesday will be given an additional travel allowance worth up to €32,535 per year.
This is on top of the standard TD's salary of €113,679, plus an additional €45,849 for being a minister of state. Super junior ministers who sit at the cabinet table receive an additional €16,000 on top of this.
Speaking on RTÉ’s This Week, Mr Canney confirmed that he had raised the question, of seeking extra expenses for junior ministers, during government formation talks.
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He said junior ministers were not entitled to the same travel allowances as TDs, and "on the basis of past experience as a Minister of State the funding we had was gone".
"The ridiculous thing was that if I had to stay in Dublin, I had to pay that out of my own pocket, whereas if I was a TD, I was given a travel and subsistence allowance for that."
"If you were going into ministerial office, you ended up with less of a financial amount of money to do more, in terms of having more expenses you had to pay out of your own pocket."
Mr Canney confirmed that the new top-up, first reported in the Irish Daily Mail, was requested during the programme for government discussions, but he said he did not make the allowance a condition of his support.
"There were no red lines on anything, the discussion around this was a very short discussion and it was not conditional."
Sinn Féin has described the new allowance as "an appalling waste of money" but Mr Canney dismissed those comments saying "it is not a new allowance, it was there, it was taken away, and we are looking for it to be restored".
The Galway TD also confirmed that he will be appointed a Minister of State with a seat at the cabinet table when the Dail meets on Wednesday.
"I have been offered the position of Minister of State in Transport, with responsibility for roads, ports, rail, and international freight."
"I will have a seat at the cabinet table, and will act as the leader of the regional ministers in government and will meet with the other two party leaders on a weekly basis prior to the cabinet meeting to discuss any issues that might be at variance with one another," he said.
"This is a partnership arrangement," Mr Canney added.
No decision on housing minister - O'Brien
Outgoing Minister for Housing Darragh O'Brien has said "nothing has been decided" when it comes to whether he will remain in the role in the next government.
However, speaking on RTÉ's The Week in Politics he said he was happy to serve in whatever capacity if asked to do so.
He said that housing is a critical issue for the country and is the "number one priority" for the government.
Mr O'Brien said the government knew that a lot more needed to be done, despite progress since 2020.
Read more: The art of the deal as Independent involvement grows
Meanwhile, Marian Harkin, Independent TD for Sligo-Leitrim, has said having additional junior ministers in additional areas was crucial for regions being able to contribute to national development, and not being an aside to the economic and social development of the country
Speaking on the same programme, she said this was reasonable and what people want.
However, Sinn Féin TD for Waterford David Cullinane disagreed and said the public did not want more junior or super-junior ministers.
He also said the Programme for Government document lacked substance and detail.
"There are lines in it that are so vague that it's laughable," Mr Cullinane added.
Neale Richmond, Fine Gael TD Dublin Rathdown said additional junior ministers are answering key political demands, and he also noted that the country's population has increased
Rory Hearne, Social Democrats TD for Dublin North-West, said that what was happening at the moment with regard to Independent TDs within the technical group wanting time on opposition benches was "frustrating" and was adding to cynicism about politics and government.
On the Programme for Government, he said that there was a lack of ambition around housing in particular.
There were no new policies and ideas, Mr Hearne added, and it was just about continuing on with the same approach.
Next govt may bring forward new Occupied Territories Bill
The incoming government will most likely bring forward a new Occupied Territories Bill, Mr Martin said, after he described the current bill as unconstitutional and deficient.
A protest urging the next government to enact the legislation is taking place at the entrance to the Ard Fheis.
Mr Martin confirmed that officials have examined the current bill and amended almost every line because it was unconstitutional and deficient.
It is likely to begin its passage thought the Oireachtas with a second stage Dáil debate.
