Transport Minister George Freeman claimed a guard “smirked and ignored” him and fellow passengers who were late for a train.
Mr Freeman, MP for Mid Norfolk, said he was due to catch the 09:09 BST from Cambridge to Attleborough but a connection from London was delayed.
On Twitter, Mr Freeman claimed the guard could see five passengers sprinting for the train but closed the doors and “waved off the train”.
Greater Anglia is investigating.
Mr Freeman had caught a Great Northern service from London King’s Cross to Cambridge, but his arrival was delayed.
He said that as he and fellow passengers “sprinted” for the train to continue their journey “the guard watched us running, closed the doors, waved off the train, leaving us stranded for an hour, then smirked and ignored us”.
Greater Anglia responded to his initial tweet to say that it could not hold services for other operators late in most cases, to which Mr Freeman said: “Not even for 15 seconds when passengers from a connection are at the door?”
The company responded: “Apologies, there should have been some discretion from the guard if that was the case but generally by rule we are not allowed to hold unless instructed otherwise.”
A spokeswoman added: “We’re sorry to hear that Mr Freeman missed his connection this morning.
“Unfortunately, his Great Northern service from London was late arriving at Cambridge station.
“We were unable to hold our Cambridge to Norwich service because it would have had a knock-on effect of causing delays to the timetable for the rest of the day on that route.”