"Several riders deliberately went through a level crossing in the town of Wallers, in violation of all safety regulations," the SNCF said in a statement.
"Millions of TV viewers have seen, live, this very serious and reckless infringement that could have been tragic."
Observing that 29 people had died in accidents around crossings last year, the SNCF said stopping trains during the race -- which is steeped in history and famed for daunting cobbled stretches -- would have caused "utter chaos".
It said the complaint was directed against "unknown persons".
On Sunday the barriers went down while the peloton was approaching at about 60kph.
Some riders managed to go through, while others stopped, but a few ignored strict race rules and swerved around the barriers seconds before the train sped past.
The International Cycling Union (UCI) described the incident as "extremely worrying" and said it had "requested a comprehensive report... for review and possible action".
The race jury decided not to sanction the riders, however.
"The riders in front could not stop in safe conditions. The second part of the peloton stopped," organisers said in a statement, explaining that the leaders had been just 10 metres away from the barriers when they started to go down.
"Consequently, the commissaires and the organisers neutralised the first part of the peloton to facilitate a regroupment with the second part of the peloton."
French champion Arnaud Demare said the cycling authorities needed to take more action.
"This needs to be taken care of, it was dangerous. We went through but it was close," he said.
The race in northern France featured 10 level crossings on Sunday and was also interrupted last year by barriers coming down as an eight-man breakaway group approached.
SNCF spokesman Christophe Piednoel said the train and the riders, who were ahead of schedule due to a strong tail wind, were not supposed to arrive at the crossing at the same time.
"We are in frequent contact with race organisers and when we can we adapt the train timetable not to disrupt the races," he said. "The train was supposed to go by 10 minutes before the riders arrived. But they were 10 minutes ahead of the earliest schedule."
Italian rider Quinziato said it would be safer to avoid railway lines but such a move would also take away some of the very features that make the race so popular and challenging.
"I understand the SNCF. There are about a dozen riders who should not have crossed," race director Christian Prudhomme told Reuters. "We need to work on a message to the riders, for their sake.'
"If we are to avoid the railway crossings, it means we must get rid of some of the cobbled sectors."