Mahinda Samarasinghe, the human rights and disaster management minister, told the Reuters news agency that "given the situation there, we are not in a position to guarantee their security".
"So they should relocate, not withdraw," he added.
There was no immediate reaction from the humanitarian community over the order, which takes immediate effect and also affects local partners of international groups.
More than 100,000 people have fled their homes in the last two years of fighting. Aid groups are bracing themselves for a similar flood from the latest battles.
The government said it was trying to avoid a repeat of the August 2006 killing of 17 local aid workers employed by the French aid agency Action Against Hunger.
Nordic truce monitors blamed the security forces for that attack but Sri Lanka's government said the Liberation Tigers of Tamil Eelam (LTTE) - fighting for an independent Tamil homeland - was responsible.
Tigers plane shot down
Monday's order comes as the military is pushing through the jungle on several fronts in a bid to surround the LTTE's headquarters at Kilinochchi, in the north of island nation.
|The 25-year-old conflict has left tens of thousands of people dead [AP]
The advance, which has seen the military claim separatist strongholds over the past three weeks, rolled forward as ground troops battled near the northwestern port of Nachchikkuda.
The air force said a separatist aircraft tried to attack a government airbase on Tuesday but was driven away by anti-aircraft fire.
Air force jets then attacked the plane and shot it down over separatist- controlled territory, Wing Commander Janaka Nanayakkara, an air force spokesman, said.
The Tigers' small fleet of light aircraft had frustrated the military with numerous attacks and the military had never before been able to shoot down one of the planes.
The air force also said it had conducted raids on three LTTE areas north of Nachchikkuda and that three separatist aircraft had bombed the government-controlled town of Vavuniya.
The government and separatists regularly accuse each other of disregard for civilian casualties.
Rights groups say both have been responsible for murders and abductions in the 25-year-old war.
Elsewhere in Sri Lanka, a journalist was shot and seriously wounded on Monday.
Police said Devakumar Radhika, a newspaper reporter, was shot by an unknown attacker in the eastern town of Batticaloa, where the government took control last year after pushing separatists out.
She had previously worked as a spokesperson for the TMVP, a breakaway LTTE faction that has since sided with the government in the east, police said.