A report in the Daily Mail said that the step came after the pilot was judged a security risk after his alleged association with the two suspected terrorists reportedly "planning to use an aircraft as part of a hostile or terrorist act."
The pilot, however, said that this was an antic and he was being suspected because of his religion and race.
The men linked with the pilot have been detained under the Terrorism Act. The pilot along with his brother, an alleged member of terror group Hizb ut-Tahrir, were arrested but were never charged.
The pilot was also questioned on the comments he made about the 9/11 attack in 2005. He had said that those killed in the attacks in 2001 were not innocent victims.