The rail firm said it was forced to suspend services on Friday night after large scale vandalism and arson took place. Two MTR staff were assaulted at Sheung Shui station.
On the East Rail line, an idle train was set on fire at Shatin station.
The rail company expressed its extreme anger over the illegal acts.
Its Chief Executive Officer Jacob Kam said it was a difficult decision to stop all services but there was no alternative if it is to provide a safe and reliable service to customers.