All trains on a line into London Kings Cross had to be cancelled at the weekend as a result of staff shortages.
First Capital Connect, which operates the Great Northern service, confirmed that not enough staff had volunteered to work overtime at the weekend.
The train drivers union Aslef denied that it had orchestrated an unofficial strike.
First Capital Connect needs up to 80 drivers to run the service, but the weekend shifts are staffed voluntarily by drivers offering to work overtime.
The union said the company had been running its weekend service recently on what it called “a lot of goodwill”.
Aslef is currently in pay talks with First Capital Connect and has already rejected two offers, the BBC reported.
First Capital Connect said: “We are continuing to work towards a resolution to these problems and to provide alternative transport where possible and will post any updates on our website.
“We regret any inconvenience this disruption will cause.”