It was unclear on Friday 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.
Police and prosecutors arrived at the gates of President Yoon Suk-yeol's compound on Friday morning. (AP PHOTO)
An arrest would be the first for an incumbent South Korean president.
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 at the gates of Yoon's compound shortly after 7am, according to Reuters witnesses.
The CIO vehicles did not immediately enter the compound, partly due to a bus blocking the driveway.
Some CIO officials later filed through an opened gate on foot and past the bus, but then briefly faced another bus and an armoured vehicle further up the driveway, before they were moved.
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 defence ministry said the troops were under the control of the PSS.
Yonhap news agency cited the head of the PSS saying the authorities were not allowed to search Yoon's residence.
As of 1pm, the stand-off continued.
President Yoon Suk-yeol sent shock waves through South Korea when he declared martial law. (AP PHOTO)
Yoon's lawyer said in a statement on Friday that execution of an invalid arrest warrant against Yoon is unlawful, and that they would take legal action, without elaborating.
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.
Some chanted "President Yoon Suk-yeol will be protected by the people", and called for the head of the CIO to be arrested.
The 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.
Yoon sent shock waves 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.
Some supporters chanted "President Yoon Suk-yeol will be protected by the people" as they rallied. (AP PHOTO)
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.
Two South Korean military officials, including army chief Park An-su who was named martial law commander during the short-lived declaration last month have been indicted after being detained by prosecutors who are investigating insurrection charges, Yonhap reported on Friday.
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's lawyers have said the arrest warrant was illegal and invalid because the CIO did not have the authority under South Korean law to request a warrant.
Yoon has been isolated since he was impeached and suspended from power on December 14.
Separate from the criminal investigation, his impeachment case is 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.
