The medical charity on Wednesday also accused the US-led forces in Afghanistan of using humanitarian aid for political purposes, in explaining its withdrawal.
The charity delivers aid in some of the world's most troubled areas, but said in a statement that poor security was "rendering independent aid for the Afghan people all but impossible".
It had been subjected to "killing, threats and insecurity," it said.
Five MSF aid workers were killed in a targeted attack in the northwest Afghan province of Badghis on 2 June, an area previously considered safe.
Belgian project coordinator Helene de Beir, Norwegian doctor Egil Tynaes, Dutch logistician Willem Kwint, Afghan translator Fasil Ahmad and driver Bismillah were killed when their Toyota Land Cruiser was attacked with grenades and gunfire.
The charity said the Afghan government's failure to conduct a "credible investigation" into the killings as well as the threat of future attacks on staff was behind their decision to withdraw from the country.
A Taliban spokesman claimed responsibility for the attacks and accused MSF workers of spying for US-led forces and said the aid agency would remain a target for insurgents.
The security situation has
worsened, says MSF
MSF said "false accusations by the Taliban" were behind their decision to pull out and also cited "the co-optation of humanitarian aid by the coalition for political and military motives," as a reason for withdrawal.
US-led coalition forces and international peacekeeping troops have set up provisional reconstruction teams (PRTs) in outlying provinces using a combination of military and civil expertise to deliver aid in places where the security situation is parlous.
Until the assassinations, MSF provided healthcare in 13 provinces with 80 international volunteers and 1400 Afghan staff.
Security around the country has deteriorated rapidly in recent months with a surge of attacks against soft targets such as government officials, aid workers and civilians in the run-up to presidential elections in October.
Insurgents from the ousted Taliban government have vowed to disrupt the election using violence, and have targeted their attacks on United Nations workers and aid workers in an attempt to undermine support for the government.
US-led coalition troops are better protected than UN and aid workers who often travel in white Land Cruisers that also make them easy to identify.