"Sea-Eye has decided to resume its rescue missions in the Mediterranean which had been halted for a month," the NGO said in a statement.
However, its two ships, the Sea-Eye and the Seefuchs, would now operate in a perimeter of 70 to 90 nautical miles from the Libyan coast, it said, "to take account of the constant threat from the Libyan coastguard and to not compromise the safety of the crews".
Sea-Eye said its decision to return was partly prompted by events on September 2, when the Seefuchs was called on to help with a rescue mission 50 miles off Libya in which 16 people in a wooden boat were saved from drowning.
"This case shows that claims by Frontex and the EU that there are no more refugees, and therefore no more drowning people, off the Libyan coast are false."
Frontex is the EU's border management agency.
Survivors last week reported that two more vessels, rubber boats filled with migrants, had set out at the same as they did, the NGO said. Those boats and their passengers disappeared without a trace.
"The deal between European countries and the Libyan coast guard is irresponsible," Sea-Eye chairman Michael Buschheuer said in the statement, because it allowed "a situation contrary to international law" to continue.
"We owe it to the people in need to stay on site and undertake rescue operations when necessary," he said.
Tensions have risen since the Libyan navy last month ordered foreign vessels to stay out of a coastal search-and rescue zone, a measure it said was specifically aimed at non-governmental groups.
Libyan authorities have accused charities of aiding human smugglers with their rescues at sea, hampering efforts to crack down on the illegal migration route.
Six years since a revolution that toppled longtime dictator Moamer Kadhafi, Libya has become a key departure point for migrants risking their lives to cross the Mediterranean to Europe.
Tens of thousands of migrants have resorted to paying people traffickers for the journey, often on overcrowded and unseaworthy boats.
Migrant aid ships have played a key role in assisting the rescue operations. Sea-Eye says it has helped save some 12,000 lives since April 2016.