Minister Datuk Seri Hishammuddin Hussein said the Charlie C130 was travelling to Labuan, Sabah, from the Subang airbase when it was intercepted.
"Yes, we have received information that the flight was intercepted by two Indonesian jets. However, we do not have full details of the incident.
"We are in the process of getting the full report," he said after distributing 1,000 of bubur lambuk (porridge) to visitors at the Setiawangsa Ramadan bazaar Sunday.
It is unclear what time the incident occurred.
Hishammuddin however assured that Indonesia and Malaysia have close relations.
"I'm not worried as this is normal and it happens everywhere in the world. If there were any incidents between us, we can deal with each other diplomatically. We will not let any incident ruin our ties.
"Plus, I am very close to the Indonesian Defence Minister, Ryamizard Ryacudu. If I need to contact him, it wouldn't be a problem," he said.
A source told The Star that the Indonesian jets were only notifying the RMAF aircraft that it had entered the Indonesian air space.
"No untoward incident occurred," he said.
The Natuna Islands are located in the South China Sea, off the northwest coast of Borneo.
Last week, Indonesian president Joko Widodo visited the islands and ordered the defence around it to be stepped up according to a report by ABC news.