Footage posted on social media showed the men, all in white T-shirts, violently attacking people on platforms and inside train carriages, the BBC reported.
At least 36 people were injured in the violence on Sunday, according to local media reports.
The mob attack followed the latest pro-democracy rally in the centre of Hong Kong, where riot police had fired tear gas and rubber bullets at protesters.
It is unclear who the mob were or what the motives for the attack were.
In a statement, the government said that in Yuen Long "some people congregated at the platforms of the MTR station and train compartments, attacking commuters".
"This is absolutely unacceptable to Hong Kong as a society that observes the rule of law. The SAR (Special Administrative Region) government strongly condemns any violence and will seriously take enforcement actions."
Hong Kong Police also said: "Some people attacked commuters at the platforms of the Yuen Long MTR station and train compartments, resulting in multiple injuries."
The mob stormed Yuen Long MTR station at about 10.30 p.m., hours after clashes between protesters and police in the Sheung Wan area earlier in the day.
Yuen Long is a more remote district of Hong Kong, and is far away from the site of the main pro-democracy protests.
Riot police fired tear gas and rubber bullets at protesters in Hong Kong at a large pro-democracy rally, and charged demonstrators who threw objects at police lines.
The protest route was altered with protesters told to stop at Wan Chai rather than Central, where the key government offices are located.
Some 4,000 police officers were deployed.
( With inputs from IANS )