Police action was necessary to pull Bahrain back from the ‘brink of a sectarian abyss,’ the Gulf Arab state's Foreign Minister Sheikh Khaled bin Ahmed al-Khalifa said.
Three people were killed and 231 wounded when police attacked anti-government protesters.
The clashes came after thousands of overwhelmingly Shia protesters took to Bahrain's streets demanding more say in the running of the kingdom.
‘The country was on the brink of a sectarian abyss so it was a very important step that had to happen, police took every care possible,’ Sheikh Khaled said.
Troops in armoured vehicles took control of Manama as part of a crackdown by the Bahraini authorities which appeared designed to snuff out protests before they could gather momentum.
Sheikh Khaled was speaking at a press conference also attended by the United Arab Emirates' foreign minister and the secretary general of the Gulf Cooperation Council, a loose economic and political bloc of Gulf Arab states.
Gulf Arab foreign ministers meeting in the Bahrain capital this evening planned to discuss the unrest in the Gulf island kingdom, state news agencies said.
Bahrain opposition activist Ibrahim Sharif told RTÉ News that the way the clearance had been carried out had maximised the danger to innocent sleeping protestors.
The Department of Foreign Affairs says there are around 200 Irish citizens living in Bahrain.
It is urging Irish people resident or on holidays in Bahrain to register with the Irish embassy in Riyadh.
This can be done online through the Department's website.
Bahrain's defence forces warned today that it would 'take all strict and preventive measures to restore security and public order', a defence ministry spokesman said in a statement.
The protestors had tried to turn the road junction into the base of a long-running protest like that at Cairo's Tahrir Square, which led to the fall of Egyptian President Hosni Mubarak.
They are demanding more say in the Gulf Arab kingdom where a Sunni Muslim family rules over a majority Shia population.
'This is real terrorism,' said Abdul Jalil Khalil, a parliamentarian from the main Shia opposition Wefaq bloc. 'Whoever took the decision to attack the protest was aiming to kill.'
The square is now nearly empty of protestors. Abandoned tents, blankets and rubbish are dotted around the area and the smell of teargas is wafting through the air.
Bahrain's Interior Ministry said on Twitter that security forces had 'cleared Pearl roundabout' of demonstrators, and that a section of a main road was temporarily blocked.
Meanwhile, a US reporter for ABC News was beaten by a group armed with clubs earlier this morning while covering the unrest, the US network reported.
Correspondent Miguel Marquez was caught in the crowd and attacked while covering protests in Manama, ABC said.
Mr Marquez, who said he was not badly injured, was clubbed while he was on the phone with his headquarters in New York describing the scene as riot police stormed through a Manama square in the dark.
'No! No! No! Hey! I'm a journalist here!' he yelled while still on the phone. 'I'm going! I'm going! I'm going! I'm going! ... I'm hit.'
He said that the men pulled his camera out of his hands.
'I just got beat rather badly by a gang of thugs,' Mr Marquez said in a later call to ABC headquarters. 'I'm now in a marketplace near our hotel where people are cowering in buildings.'
