A UN official said on Saturday that the SPLA was withdrawing to the south and that the SAF had started to withdraw its forces on Friday.
The rival armies had missed a June 30 deadline to leave, and Abyei residents have failed to return to the deserted town.
Abdel Rahman Mohamedai, the spokesman for the northern army of the Joint Defence Board (JDB), said: "We began today to withdraw parts of our force."
The JDB is the body created by an accord which ensures co-operation from both northern and southern armies.
On Thursday, the SPLA had said it had almost completed its withdrawal, but was concerned that the SAF was delaying.
"In less than three days, we will finish the redeployment," Pieng Deng Kuol, the SPLA's head of operations, said:
Mohamedai said the delay in withdrawing the northern forces was because they were waiting for police and for a temporary administration to take power.
Major-General Daniel Parnyang, of the SPLA, said there had been a misunderstanding over whether the forces were supposed to withdraw from the wider Abyei area or from Abyei town.
"The withdrawal is out of Abyei area - their forces are inside, ours are along the border, but outside," he said.
But a spokesman from the SAF said that the SPLA forces did not withdraw, and criticised them for "interfering" in the business of Omar al-Bashir, the Sudanese president, and Salva Kiir, the first vice-president, who is the leader of the south.
"The SPLA did not withdraw their forces. They are only south of the Bahr al-Arab river. The process of [us] withdrawing is ongoing and gradual," the spokesman said.
Kiir and al-Bashir signed an agreement on June 8, which would allow a joint integrated military unit of 600 soldiers to deploy in Abyei by June 18 to restore security after the recent fighting sparked fears of a new civil war.
The north and south are still discussing who will make up an interim administration for Abyei, but have agreed on international arbitration to settle the dispute.
Abyei is to hold a referendum in 2011, on whether to retain its special administrative status in the north or join the south, which could decide in a separate referendum to secede from the north.
The May fighting was seen as the biggest threat to the peace process that, in 2005, ended 21 years of civil war between north and south.