Pyongyang said it downed a surveillance drone in early January, accusing Seoul of sending the aircraft to gather intelligence on "important targets".
South Korean authorities raided the country's intelligence agency on Tuesday as part of a probe into an alleged drone incursion into North Korea, an episode that could undermine Seoul's efforts to improve ties with Pyongyang.
North Korea has said it shot down a surveillance drone near the industrial hub of Kaesong in January, accusing its neighbour of trying to glean intelligence on "important targets".
Seoul denied any official involvement, with South Korean President Lee Jae-myung saying such an act would be tantamount to "firing a shot into the North".
But a joint military-police task force said on Tuesday it was investigating three active-duty soldiers and one spy agency staffer to "thoroughly establish the truth".
South Korean investigators raided 18 locations of interest, including the Defence Intelligence Command and the National Intelligence Service.
Political tightrope
North Korea's army said it downed a drone carrying "surveillance equipment" in early January, according to a statement by the state-run Korean Central News Agency.
Photos published by the agency showed the wreckage of a winged craft on the ground next to a collection of grey and blue components that allegedly included cameras.
The drone had stored footage of "important targets" including border areas, a North Korean military spokesman said in the statement.
South Korea's disgraced ex-president Yoon Suk-yeol was previously accused of using unmanned drones to scatter propaganda leaflets over North Korea in 2024.
Lee has vowed to mend ties with North Korea by stamping out such provocations, and has even suggested a rare apology may be warranted.
"I feel I should apologise, but I hesitate to say it out loud," he said in December.
"I worry that if I do, it could be used as fodder for ideological battles or accusations of being pro-North."
South Korea's Unification Minister Chung Dong-young has previously suggested that the alleged incursion may have involved officials still loyal to former hardline leader Yoon.
Three civilians have already been charged for their alleged role in the drone scandal.
One of them has publicly claimed responsibility, saying he acted to detect radiation levels from North Korea's Pyongsan uranium processing facility.
Yoon on trial
Ex-president Yoon is currently standing trial on charges he illegally sent drones into North Korea to help create the pretext for declaring martial law in late 2024.
Prosecutors have accused Yoon of instructing Seoul's military to fly drones over Pyongyang and distribute anti-North leaflets in an attempt to provoke a response.
They said Yoon and others "conspired to create conditions" that would allow him to tighten his grip on power by declaring martial law.
Yoon's disastrous attempt to overturn civilian rule ultimately failed.
The 65-year-old was impeached and ousted from office in April last year.
Last month, Yoon was sentenced to five years in prison in the first verdict from eight criminal trials over the martial law debacle and other allegations.