Migrants on board a government-chartered tourist boat off Malta occupied the kitchen, grabbed knives and threatened to blow up a gas cylinder and burn rubbish, Prime Minister Robert Abela said on Sunday.
"They gave us half an hour to act or they would kidnap the crew," he said.
The migrants had been left out at sea for more than a month, sparking protests from humanitarian organisations.
Describing the dramatic situation, he told a One News interviewer that up until Saturday morning, the government had not planned to bring in the migrants being held offshore on board four tourist boats.
But he said he had to take a decision after the crew (on board Europa II) called for help, even calling him personally pleading 'Please save us'.
He said the easiest choice would have been to board the boat with force, take control and stop the situation. But the AFM had warned him of a risk of soldiers and migrants possibly being injured or killed.
Abela said he could not risk lives or losing control.
He said another consideration about bringing the migrants to Malta was the length of time they had been at sea.
Some of them had been at sea for 40 days, he said. Malta had done its duty by rescuing them and giving them basic conditions.
But even people on a luxury cruise ship would not stick 40 days at sea, especially on small vessels in a rough sea state.
Abela also hit out at the European Union for having ignored the plight of the migrants. Malta was criticised for not being humane, but he asked his European partners what they had done.
Malta was left alone to deal with a complex problem which was not its own.
Abela said going to Libya last week was a serious risk and was even given a bullet-roof vest.
Abela said EU solidarity was inexistent.
Some EU states had said they were prepared to take migrants, but only after they were allowed to land in Malta. He would now vigorously follow up those pledges, he said.