German NGO Sea-Watch said the Moonbird aircraft has been blocked from taking part in refugee rescue missions.
The Moonbird aircraft is jointly operated by Sea-Watch and the Swiss Humanitarian Pilots Initiative (HPI) with support from the Evangelical Church of Germany.
Together with the Sea-Watch 3 ship, Moonbird participated in the rescue of some 20,000 people last year, the German NGO said in a media release.
But with Sea-Watch ships impounded and the Moonbird grounded, rescue missions were no longer possible, the NGO said.
"The consequences of this ban on flights should be clear to those politically responsible. The people on those boats won’t be rescued but will instead drown out of sight," said HBI pilot and founder Fabio Zgraggen, who is from the eastern Swiss region of Appenzell.
The Moonbird operated in the area north of the Libyan coast for two years without problems before missions were grounded, according to Zgraggen.
He told Swiss news site Watson that Maltese authorities had blocked HPI rescue flights because there had been no request from Malta or Italy for those operations to go ahead.
But the 33-year-old said no permit was required to operate private rescue flights.
Zgraggen said a lawyer had been taken on and the plan was to get flights back in the air as soon as possible.
The Moonbird ban comes as Italy and Malta ramp up efforts to stop NGOs from using the island nation of Malta as a base of operations for the rescue of refugees off the Libyan coast. Italy's interior minister has also said that Italian ports will be closed "all summer" to NGO migrant rescue boats.
After a recent EU summit on immigration, the European Council appeared to back Italy and “other frontline Member States” in the fight against people smuggling.
“All vessels operating in the Mediterranean must respect the applicable laws and not obstruct operations of the Libyan Coastguard,” said the European Council in a statement.