The plane is owned by Phillip Morse, 69, the vice-chairman of New England Sports Ventures, which bought the club on Friday for £300million.
An investigation has established that between 2002 and 2005 the CIA chartered the plane from Mr Morse for millions of pounds and made extensive use of it.
Inquiries by the European Parliament and human rights groups have linked the plane to alleged extraordinary rendition operations which took place during the same period.
A European Parliament report linked the jet directly to the abduction of Abu Omar, an Islamic preacher, who was snatched from a Milan street by the CIA in 2003 before being taken to Cairo.
Extraordinary rendition entails the abduction and transfer of a terrorist suspect from one country to another. People have been taken to states such as Egypt, Syria, Morocco and Uzbekistan which are suspected of practising torture in violation of a United Nations Convention.
The disclosure that such a senior figure in New England Sports Ventures (NESV) has been paid millions by the CIA is likely to alarm football fans already concerned that one of the country’s most prestigious clubs is still in American hands.
Mr Omar was snatched by the CIA in 2003 despite having been granted political asylum by the Italian government. He was moved to an American air force base at Aviano near Venice before being transported to a NATO base in Ramstein in Germany. He was then flown from Germany to Cairo.
The European Parliament report reproduced flight documents for Mr Morse’s jet, which carries the logo of the Boston Red Sox baseball team, also owned by NESV, on its tail fin. The 19-seater Gulfstream IV, with the registration N85VM, flew from Washington to Ramstein on February 4, 2003.
On February 17, the day of Mr Omar’s abduction and rendition, the plane left Ramstein at 6.52pm and arrived in Cairo at 10.30pm. The following day the plane made the return journey to Washington via Shannon in Ireland.
MEPs and European rights campaigners believe the plane may have been used in other rendition operations. They point out that its travel destinations, which are detailed in flight logs, are totally at odds with those expected of a normal private charter jet.
During the same period it was on loan to the CIA the jet flew to Kabul in Afghanistan, Rabat in Morocco, Tripoli in Libya and Baku in Azerbaijan. The jet, which changed its registrations details in December 2004 to N227SV, also made at least 51 trips to Guantanamo Bay, Cuba.