Yassar Yaqub, 28, from Huddersfield, was shot by an officer in an operation near junction 24 on 2 January.
Moshin Amin, 30, Broomer Street, Dewsbury, denied possessing a handgun, a silencer and ammunition with intent to endanger life at Leeds Crown Court.
A provisional trial date was set for 4 December and Mr Amin was bailed until 27 June.
A man driving a car in which his passenger was shot dead by police on the M62 has appeared in court.