Two Australians have agreed to pay a fine for flying in Indonesian airspace without permission.

Two Australians have agreed to pay a fine for flying in Indonesian airspace without permits, but will not be free to leave the country immediately.

Indonesian air force jets had their weapons locked on the small plane piloted by Graeme Jackline and Richard MacLean when they forced it to land in Manado, Sulawesi, on Wednesday morning.

One of the Sukhoi pilots, Major Wanda Suriansyah, said he had locked a target on the Australian plane because it had refused to land for four hours.

“If there was an order to shoot, I could immediately shoot,” he told Indonesian news website Tempo.

“But thank God, the pilot finally got scared and landed in Manado.”

The Australians were on a delivery job, taking a small 1966 Beechcraft twin-engine plane from Darwin to Cebu in the Philippines, when they were intercepted by two Indonesian jets.

On landing at Sam Ratulangi Airport, Manado, about 20 air force and airport officers swarmed the aircraft.

A witness, Adolof, said about half of them had weapons.

“They were laying on the ground while waiting for the plane to land,” he said.

“After it landed the pilots came out and were searched.”

The Australians looked annoyed as they were ordered off the plane and frisked, he told AAP.

“When they got off the plane they were taken to the office, then airport staff took documents from the plane,” he said.

Consular assistance was provided to the men, the Department of Foreign Affairs and Trade says.

After investigations, they had agreed to pay a fine of Rp 60 million ($A5670), airport spokesman Syaifullah Siregar said.

“Yes, they have admitted their mistake and are ready to pay the fine as per our regulations,” he said.

“But before paying the fine, we still must wait for a security clearance.”

Air force spokesman Brigadier General Hadi Tjahjanto says the clearance should take 24 hours.

With the fine paid and the clearance issued, the Australians will be free to go.

“When we forced down the plane, they didn’t have several documents,” he said.

He said they need a security clearance issued by Air Force Headquarters and a flight clearance from the Aviation Transportation Directorate General.

“When all the requirements needed for those clearances are complete, it will only take a day to be issued, depending on the requirements they have.”

The plane’s owner, Mr MacLean, is an experienced pilot and used-aircraft salesman who operates Australian Aircraft Sales in South Australia.

His wife, Kaye, said he had completed aircraft deliveries around the world and understood the airspace permissions required, suggesting the incident could be a simple paperwork mishap.

“I think there’s a misunderstanding,” she told Fairfax Media.

Small aircraft are commonly sold internationally and delivered by air, but airspace permissions are required when flying through a country’s territory.