The International Committee of the Red Cross (ICRC) spokesperson Sarasi Wijeratne said that ICRC officials withdrew from the security exit and entry point at Omanthai in the northern Vavuniya district.
However, she said that ICRC's operations in the rebels' areas would continue as normal.
ICRC officials are to make a further assessment on Thursday to see if they could return to the check point, officials added.
ICRC facilitates the transfer of bodies of combatants between LTTE (Liberation Tigers of Tamil Eelam) rebels and government troops and the transport of the sick among the civilians.
It is learnt that the withdrawal decision was based on security reasons.
The ICRC announcement came just 24 hours after the military decision to restrict the opening hours of the Omanthai security check point.
The military said that the check point would be opened between 9 a.m. and 1 p.m. local time (0330 to 0730 GMT) with effect from Wednesday.
It was usually opened between 9 a.m. to 4 p.m. local time (0330 to 1030 GMT).
Udaya Nanayakkara, the military spokesman said that the check point could not function without the presence of ICRC officials.
Analysts said the decision to restrict opening hours of Omanthai and the ICRC's decision to stay away may have been forced by fighting along the A9 highway.