They provided covering gunfire as at least nine commandos lowered themselves by rope onto the roof of Nariman House from an Indian air force helicopter.
It was not immediately clear if there were hostages in the building or their fate.
Two workers and a child escaped from the building on Thursday, the only people to emerge so far.
The child was identified as Moshe Holtzberg, two, the son of Rabbi Gavriel Noach Holtzberg, the main representative at Chabad house.
Still holed up
Elsewhere in Mumbai, commandos searched two luxury hotels which police said fighters were still occupying along with an unknown number of hostages.
Sporadic gunfire and explosions are still being heard in and around the Taj Mahal Palace and the Trident-Oberoi hotels.
At least 93 people, most of them foreigners, were evacuated from the Trident early on Friday, police said.
However, it appears that attackers inside the Taj hotel are still resisting security forces, Sohail Rahman, Al Jazeera's correspondent in Mumbai, said.
"Earlier it had been reported that security services had been able to take control of the Taj, but [as of about 0900 GMT] there was shooting from the second and third floors of the hotel, from gunmen holed up there," he said.
"Security services fired back but they have now restrained themselves because they believe there are a number of hostages still inside.
"That is quite a surprise considering that a few hours ago it was reported that they had control of the hotel and the Taj siege was over."
The chief of India's Marine Commando Force said on Friday that his troops had come across "12 to 15 bodies" while sweeping through the Taj.
"The [attackers] were the kind of people with no remorse - anybody and whomsoever came in front of them, they fired," the commando, who was wearing a black mask, said in a news conference.
"We could have got those terrorists but for so many hotel guests … The bodies were lying strewn here and there. There was blood all over and in trying to avoid the casualty of those civilians, we had to be that much more careful," he said.
Ratan Tata, who runs the company that owns the Taj Mahal hotel, said the attackers had detailed knowledge of the layout of the buildings.
The strikes by small bands of armed men starting on Wednesday night shocked Mumbai, the nerve-centre of India's growing economic might and home to the Bollywood film industry.
At least eight foreigners, including an Australian, a Briton, an Italian and a Japanese national, have been killed.
Seven attackers have been killed and nine suspects taken into custody, police have said.
Twelve policemen, including the head of Mumbai's counter-terrorism force, have also been killed, police say.
Al Jazeera's Riz Khan, reporting from outside the Trident-Oberoi, where gunfire had been heard throughout Thursday, said things were quiet just before dawn on Friday.
Referring to the Trident hotel, Rahman said there has been "very little activity from the security personnel as far as we know".
|Mumbai, a financial hub popular with tourists, is reeling after the attacks [AFP]
"[On Friday] there was a sound of a very large thud and people wondered whether there was some sort of military operation ongoing; whether they [security forces] were going to take the hotel," he said.
"It's been very unclear what stage the security personnel have been able to sweep the hotel.
"They started over 12 hours ago on Thursday combing room by room, floor by floor, trying to secure the building before they can catch the attackers still holding those hostages."
Indian government officials have been "very tight-lipped about the progress of the special forces at the locations where these attacks have happened", our correspondent said.
"They are only giving out information as and when they can confirm it. They are making sure that they have a very tight lid on the information that is filtered out to the media," he said.
"So it is very difficut to asses exactly at what stage any of these forces or government officials are at in terms of planning in retaking buildings."
A US investigative team is heading to Mumbai, a state department official said on Thursday evening.
Meanwhile, the Indian media, citing unidentified police investigators, reported on Friday that three alleged attackers had confessed to being members of Lashkar-e-Tiyaba, a Pakistan-based group which aims to end Indian rule in Kashmir.
Lashkar-e-Tiyaba had earlier denied any role in the attacks.
The Hindu newspaper said interrogation of the suspects revealed that Lashkar operatives had left Karachi in Pakistan in a merchant ship early on Wednesday and went ashore at Mumbai on a small boat before splitting up into teams to attack multiple locations.
|India pressed anti-terror commandos into action after the attacks [AFP]
Earlier, a little known group calling itself the Deccan Mujahidin claimed responsibility for the attack in emails to news organisations.
Dipankar Banerjee, a retired Indian general, told Al Jazeera that he does not rule out the possibility that the Indian Mujahidin, blamed for previous attacks, were responsible for the Mumbai assaults.
In a speech on Thursday, Manmohan Singh, the Indian prime minister, blamed "external forces", a phrase sometimes used to refer to Pakistan-based fighters.
Mahan Abedin, an insurgency analyst, told Al Jazeera: "We have seen an increase in recent years in indigenous Indian Muslim organisations beginning to take a violent stance towards the Indian state and sections of the Indian society, particularly the commercial elite of places like Mumbai, in order to highlight, they would say, the sheer inequality of life in India.
"There is a middle class of around 100 million who live very well but 800 million-plus people live in miserable conditions."
Pakistan, for its part, has condemned the attacks and has said it will fully co-operate with an Indian investigation.