Rescue teams dug through thick mud and debris in search of bodies in Tacloban City, the capital of Leyte province.
Some of the dead that had been recovered were left along the streets, waiting for body bags.
At least 2,357 people were confirmed dead after Haiyan ripped through the Philippines on November 8, flattening cities and towns, the national disaster relief agency said.
"We are moving as fast as we can because the people are really complaining to us," said Alfredo Gimao, a rescue worker from Manila.
Defence Secretary Voltaire Gazmin said that the retrieval of bodies had been hampered by the destruction caused by Haiyan's ferocious winds in Tacloban as well as other affected areas.
"We do have a problem because of the debris," he told reporters. "We started retrieving bodies two days after the typhoon ... We had to prioritize the living rather than the dead," he explained.
Many survivors have been complaining about the foul odour, and expressed fears that it could make them sick, despite assurances from health officials that the dead bodies were unlikely to cause widespread disease.
"We want to leave because we are afraid that people will start getting sick," said Omar Fumar, a 39-year-old security guard who was camped out at Tacloban's airport with 10 other relatives. "It is so dirty here now and so many dead bodies have not been cleared." Fumar, a father of three, said he was most worried about diseases that could spread from the lack of potable water and sanitation.
"I don't want my kids to get sick, they've already been through alot," he added.
More than 11 million people were affected by Haiyan's destruction, including nearly 600,000 displaced badly needing food, water and shelter, according to the United Nations' humanitarian affairs office.
Soldiers were distributing water and rice from trucks in Tacloban City, where hungry survivors had looted supermarkets, shopping malls and drugstores.
Eduardo Del Rosario, head of the national disaster relief agency, said more relief workers and supplies were en route to the affected areas, not just Tacloban City, amid complaints from other areas that they have been ignored.
"We have a concrete system for relief operations, but we weren't prepared for this magnitude," he told reporters in Manila. "This is very big." Del Rosario said the air force had started air dropping relief goods to areas unreachable by land.
Nearly 4,000 people were injured in Haiyan's onslaught, while at least 77 were reported missing, the national disaster relief agency said. Damage to infrastructure and agriculture was estimated at over4 billion pesos (94 million dollars).