It came hours after divers recovered the first body from the petty officers' mess hall of the sunken 1,200-tonne corvette Cheonan, Yonhap news agency said, citing military officials.
"We called off a rescue operation scheduled at 11 pm (1400 GMT) following the request from the relatives. From Sunday we will focus on salvaging the wreckage," a navy spokesman was quoted as saying by Yonhap.
The 88-metre warship went down on March 26 following an unexplained explosion which tore the vessel in two near the disputed maritime border with North Korea.
A total of 58 people were rescued from the bow section of the ship soon after the sinking but efforts to locate the missing 46 crew have been hampered by bad weather and strong currents.
A week after the disaster, officials are still searching for answers as to what caused the ship to break in two in the murky waters off Baengnyeong Island in the Yellow Sea.
Defence ministry and presidential officials have dismissed media reports that the ship had been tracking North Korean submarines at the time.
Defence Minister Kim Tae-Young said Friday a torpedo might have sunk the warship but did not indicate who might have fired one.
Seoul has not cited any evidence the North was involved, although the defence minister earlier in the week said a North Korean mine -- either drifting or deliberately placed -- might have caused the disaster.
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