Police are investigating after a bus driver was allegedly followed by a cyclist into a Brisbane depot and assaulted on Tuesday evening.

The 49-year-old man was driving a council bus along Jephson Street at Toowong when an incident involving a cyclist occurred about 8.40pm.

The cyclist then followed the driver to the Toowong bus depot and allegedly assaulted the driver before riding off, police said.

The driver suffered a cut to his lip and above his eye and on Wednesday morning went to Indooroopilly police station, where he filed a formal complaint.

Rail Tram and Bus Union spokesman Tom Brown said according to the bus driver, the earlier incident on Jephson Street involved the cyclist cutting in front of the bus.

“He (the driver) said he didn’t know (what happened), all of a sudden this guy cut in front of him and he had to slow down,” Mr Brown said.

A police spokeswoman said an incident did occur prior to the alleged assault but could not confirm what happened.

Mr Brown said it was worrying the cyclist had been able to get through the depot's security gates.

“(The cyclist went) through the security gates, followed him to where the driver parked the bus,” Mr Brown said.

“He got in the bus as the driver did the check down, checking for lost property."

It is understood the driver would be off work for a couple of days.

“He will go for counselling and go to his doctor,” Mr Brown said.

“He was glad we were there to support him today at Toowong when he came down to fill out the paperwork.”

This is the second alleged attack on Brisbane bus drivers in less than a week after a 67-year-old driver was headbutted on a bus at Mount Gravatt East on Saturday night.

Brisbane City Council bus drivers will strike on Thursday between 10am-2pm and 6pm-10pm.