Major Clinton O'Neill, the spokesman for the Maltese army rescue co-ordination centre, told Al Jazeera on Sunday that the Pinar was diverted to make the rescue after it was identified as the nearest vessel.
"We then instructed the ship to proceed to the nearest safe haven. It was Lampedusa," he said.
Italy had insisted that the Pinar was in Malta's search and rescue area, arguing that Malta should have accepted the migrants. But Malta repeatedly refused.
"I've asked and continue to ask Malta to accept its responsibilities which it undertook according to international treaties," Roberto Maroni, the Italian interior minister, was quoted by state news agency ANSA as saying on Friday.
But Tonio Borg, Malta's foreign minister, told Al Jazeera that international law "provides that Malta coordinates the search and rescue and then the migrants go to the country closest to which they were received".
"They were three times closer to Lampedusa than to Malta, so I cannot understand why authorities are saying we should have accepted these migrants," he said.
Two migrants who were ill were flown by an Italian military helicopter to Lampedusa on Friday night. One person had already died before the Pinar reached the two boats.
O'Neill said that there was no immediate threat to any of the migrants who remained on the vessel.
"The ship is in contact with Italian authorities as well as us. We know for sure they [the migrants] don't have any medical problems and they have food and water on board," he told Al Jazeera.
But Italian news reports conflicted with O'Neil's statements, reporting that some of the migrants onboard were infected with chicken pox.
A spokesperson for the Italian coastguard said that military helicopters had taken water, blankets and food to the people onboard the Pinar.
In March, Malta refused entry to an Italian frigate which had rescued migrants off Lampedusa. They were later taken to Italy.
Each year, tens of thousands of migrants pay smugglers to try to reach Italian shores. Often their boats capsize or get stranded, and nearby fishing boats or military ships rescue them.
The number of illegal migrants arriving in Italy by boat rose by 75 per cent in 2008, reaching 36,900 people.
Malta, which has a population of around 350,000, has also seen an an upsurge of arrivals with around 500 migrants arriving since the beginning of the year.
It says that as a proportion to its population, migrant arrivals are higher than in any other country and are straining the country's social structure.