It was unclear whether the Presidential Security Service (PSS), which has previously blocked access by investigators with a search warrant to Yoon's office and official residence, would try to stop him being arrested.
Yoon is under criminal investigation for insurrection over his December 3. martial law attempt that stunned South Korea, Asia's fourth-largest economy and one of the region's most vibrant democracies.
An arrest would be unprecedented for an incumbent South Korean president.
Supporters of President Yoon have staged a protest outside the presidential residence. (EPA PHOTO)
Officials from the Corruption Investigation Office for High-ranking Officials (CIO), which is leading a joint team of investigators that include the police and prosecutors, had arrived gates of Yoon's compound shortly after 9am AEDT, according to Reuters witnesses.
Once inside the compound, the CIO and accompanying police faced cordons of PSS personnel, as well as military troops seconded to presidential security, media reported. South Korea's Ministry of National Defense said the troops were under the control of the PSS.
Yonhap news agency cited the head of the PSS saying the authorities are not allowed to search Yoon's residence.
Yoon's lawyer said in a statement that execution of an invalid arrest warrant against the president is unlawful, and they will take legal action, without elaborating.
Broadcaster YTN reported that about 2800 police had been mobilised in preparation for executing the warrant.
Protesters gathered in the pre-dawn hours near the residence, with the numbers swelling into the hundreds amid media reports that investigating authorities would soon try to execute the arrest warrant that was approved on Tuesday after Yoon refused summons to appear.
"We have to block them with our lives," one was heard saying to others. About a dozen protesters tried to block a group of police officers at the entrance to a pedestrian overpass.
A heavy police guard kept Yoon's supporters at bay during Friday's arrest attempt. (AP PHOTO)
The current arrest warrant is viable until January 6, and gives investigators only 48 hours to hold Yoon after he is arrested. Investigators must then decide whether to request a detention warrant or release him.
Once arrested, Yoon is expected to be held at the Seoul Detention Centre, Yonhap News Agency said, citing the CIO.
Yoon sent shockwaves through the country with a late-night announcement on December 3 that he was imposing martial law to overcome political deadlock and root out "anti-state forces".
Within hours, however, 190 MPs had defied the cordons of troops and police to vote against Yoon's order. About six hours after his initial decree, Yoon rescinded it.
He later issued a defiant defence of his decision, saying domestic political opponents are sympathetic to North Korea and citing uncorroborated claims of election tampering.
Kim Yong-hyun, who resigned as Yoon's defence minister after playing a major role in the martial law decree, has been detained and was indicted last week on charges of insurrection and abuse of power.
Insurrection is one of the few criminal charges from which a South Korean president does not have immunity.
Yoon has been isolated since he was impeached and suspended from power on December 14.
Separate from the criminal investigation, his impeachment case is currently before the Constitutional Court to decide whether to reinstate or permanently remove him.
A second hearing in that case is scheduled for later on Friday.
