Séan Canney has decided to leave the Independent Alliance group but will continue to support the Government on issues of confidence and budgetary matters.
In a statement, Mr Canney said he took time to consider all his options before he made the decision.
The alliance was formed in January 2015, in the Dáil its members are John Halligan, Finian McGrath, Shane Ross and Kevin 'Boxer' Moran.
In recent weeks it emerged that the Galway East TD was unhappy that the group was unwilling to rotate the Minister for State role at the Office of Public Works for a second time.
The position is currently held by Kevin 'Boxer' Moran who has received the backing of his colleagues to stay in the job until the next election.
Mr Canney held the role for the first year of the current Government before it rotated to his Alliance colleague.
Speaking on RTÉ's Today with Sean O'Rourke, Mr Canney said the deal "was rotating and by definition that says what it is."
He said he had lost trust in the Independent Alliance as a group, saying "when you shake hands with a man on a deal and the deal doesn't come through you have to ask if the trust is gone."
He held a private meeting with Taoiseach Leo Varadkar two weeks ago.
The Independent Alliance issued a statement saying it notes the departure of Mr Canney from the group and "we wish him well in the future."
Mr Canney has said that he is now an Independent TD supporting the Government and will deal directly with the Taoiseach.
Whether or not he remains Assistant Government Chief Whip is the prerogative of the Taoiseach, he said.
He added that his priority is implementing the Programme for Government.
Speaking at an event in Dublin this morning, Mr Varadkar said he deeply regretted Mr Canney's resignation and that whether he remains as Assistant Government Chief Whip will be decided next week.