Robert Abela said it was a difficult decision to demand Kusi Dismark's return to Ghana and admitted that a decision on his status could have been taken earlier.
"Like most people, I strongly felt for his humanitarian needs, and it's a difficult decision when you come to it because people like him always have a tragic story behind them," he said.
"Could we have come to that decision earlier? Yes, but we weren't sleeping on these situations either."
The Prime Minister was fielding reporters' questions as Kusi was being flown to Ghana on Friday.
Kusi, 37, left after 13 years in the country, despite calls for appeals for reconsideration on humanitarian grounds.
He decided to voluntarily return to Ghana after being detained on January 21 on the strength of a removal order.
Abela said every migrant has a tragic story behind them - otherwise, they would not attempt the perilous crossing - but it would be dangerous for the country to allow all of them to stay for that reason only, or simply because they had been in the country for a long time.
"You have a tragic human story if you've decided to leave Libya with 40 people on a boat that fits only 10, and then make a 200 nautical mile crossing amid storms and the risk of shipwreck," he said.
"All of them have a tragic story, but if we had to decide who stays and works in the country based on whether they have a tragic story, then we would be completely opening up our doors with no return policies.
"We must observe the rules, and in doing that, we have always treated people with dignity."
As a person who was denied asylum when he landed in Malta in 2011, Kusi was allowed to work and pay taxes and social contributions.
He paid for his studies, opened a hair salon in Ħamrun and planned to expand his business until he was arrested on January 21. Kusi was detained as he was subject to a removal order dating back to June 2011.
On Friday his lawyers told Times of Malta he will not face a ban to enter Malta following the "intervention" of the Home Affairs Ministry.
Shortly afterwards Abela told reporters Kusi's was not a one-off case - it was part of an ongoing process through which the authorities identify people living irregularly in Malta.
Asked why Kusi could not have been allowed to live and work in Malta when the country needed so many workers anyway, Abela said that would be a "dangerous" policy.
The country's economic growth did need foreign workers, but only in certain sectors.
"This country cannot welcome every foreigner who decides to come here. We welcome those who have skills that our employment market needs," he said.
"This surely cannot be a free-for-all situation."
Abela also stressed the government never left migrants in Malta's search and rescue zone to die at sea and always rescued them and treated them with respect.
In September 2022, a four-year-old migrant girl - Loujin Ahmed Nasif - allegedly died of thirst while stranded on a boat in Malta's search and rescue zone - three days after the Maltese authorities were allegedly contacted to save the migrants.
Asked about Loujin and how her story contrasts with images seen earlier this week of prominent politicians welcoming and embracing three-year-old Palestinian girl Selah Hajras, who was brought to Malta for urgent medical help after having been injured in Gaza, Abela said the cases do not compare.
It was not the responsibility of the Maltese authorities to save Loujin, but of "another EU state", he said.
Meanwhile, the government will continue to collaborate with the Palestinian ambassador to bring over more children from Gaza for medical help.