A bus driver was also injured during an attempted hijacking amid another night of trouble linked to the flag dispute.
Police said officers were called to the Lower Newtownards Road after reports that petrol bombs were thrown from Pitt Park towards St Matthew's Church in Bryson Street in the nationalist Short Strand area.
When they arrived they came under attack from crowds throwing petrol bombs and stones.
One officer was injured and water cannons were used.
A statement from the PSNI said: "There was then an exchange of stones and other missiles between two factions until police restored order. One officer is reported to have been injured.
"Police resources remain at the scene due to ongoing disorder with the objective of maintaining public safety."
A 17-year-old man has been arrested in connection with the trouble.
Meanwhile a bus was attacked by stone throwers on the Newtownards Road at around 7.25pm.
It is understood the driver has been taken to hospital with cuts to the face. Translink said all Metro services were withdrawn in east Belfast "due to two separate incidents" on Monday night.
In another separate incident, two men aged 28 and 69 were arrested amid disorder following a street protest at Great Victoria Street earlier in the evening. And in Ballymena, a 16-year-old man was arrested following a protest in the Larne Road Link area.
Sinn Féin Councillor Niall Ó Donnghaile said a group of special needs children had to flee St Matthew's Church on Monday night.
He said: "This evening homes on Strand Walk came under petrol bomb attack from a unionist crowd on the Newtownards Road. A special needs group were forced to flee from St Matthews Parochial Hall.
"This was a blatant, well planned and organised sectarian attack on this community from those gathered on the Newtownards Road.
"It has nothing at all to do with flags or identity. It is an attempt by unionists to intimidate a small catholic community."
There have also been a number of reports that homes in Pitt Park and Susan Street on the unionist side of the interface have come under attack.
Loyalist community worker Jim Wilson, who said loyalist youths were involved when the trouble began, blamed outside elements.
He said: "I swerved around a group of around 20 young lads at the bottom of the Newtownards Road and they were attacking homes with bricks and bottles.
"Police landrovers came on the scene and were pushing them back when 20 or 30 petrol bombs came over the landrovers. About 300 nationalists came up to the end of Bryson Street and we were very fearful but police went down Bryson Street and pushed them back."
The disturbances are linked to the ongoing dispute over the flying of the Union flag at City Hall.
Earlier PSNI Chief Constable Matt Baggott defended police tactics after violence flared in east Belfast on Saturday as loyalist protesters returned from a city centre demonstration past the Short Strand area.
He also warned rioters involved in the ongoing trouble that they will get caught.
"For those who remain committed to rioting and violence, I would say this - don't make it worse because the knock on the door is coming," he said on Monday.
Around 100 police officers have been hurt since the start of the flag dispute last month, while over 110 people have been arrested.
It comes after Belfast councillors voted at the start of December to restrict the flying of the Union flag over City Hall to 18 designated days.