Twenty-nine people were arrested as Newcastle United supporters clashed with police in ugly scenes that cast a further shadow over English football after an outbreak of serious violence between Millwall fans at Wembley.

After an intense north-east derby at St James' Park between Newcastle United and Sunderland on Sunday afternoon, which Newcastle lost 3-0, supporters threw glass bottles, firecrackers, bricks and rocks at police, with one officer reportedly saying: "This is the worst rioting I have seen in the city centre in decades."

One Newcastle fan was seen to punch a police horse and wheelie bins were set alight as supporters rampaged through the streets. The most serious incident occurred when a group of Newcastle supporters tried to confront their Sunderland counterparts at the city's Central station. During the fracas three officers were injured and one required hospital treatment.

The Northumbria police chief superintendent, Steve Neill, said: "Disappointingly, there was some disorder involving what appear to be Newcastle United supporters following the match in the city centre, including an incident at Central station. Disruptive behaviour of any kind is not tolerated. Inquiries will take place into these incidents and action will be taken against all those involved.

"Public safety is always our number one priority during any football match. For those who chose to get involved in disruptive behaviour they were either dealt with swiftly by officers or will be subject to retrospective action at a later date."

The violence came despite the authorities warning fans ahead of the match to be on their best behaviour, realising the potentially volatile nature of the fixture. Newcastle and Sunderland are fierce local rivals and the result, Sunderland's first win at the stadium in 13 years, appears to have sparked the trouble.

Police also warned supporters in the build-up to the match to refrain from political gestures that might incite hostility as the new Sunderland manager, Paolo di Canio, has previously declared his fascist beliefs.

Hooliganism has been reduced at football matches in recent years but ugly clashes at Wembley on Saturday, as well as Sunday's trouble on Tyneside, were a stark reminder that the problem has not been eradicated.

Millwall fans fought between themselves during their FA Cup defeat to Wigan Athletic, with the Metropolitan police making 14 arrests and four officers receiving minor injuries.

Images of fans with bloodied faces and young children crying at the national stadium were broadcast live on TV.

A spokesman for the south London club said: "We are devastated by the scenes we saw yesterday, which are in danger of undoing much of the good work we have done to try and change the perception of the club. We are trying to find the answers to what happened."

Of the 14 arrests at Wembey – 12 of which were Millwall fans – four were for affray, one for affray and possession of class A drugs, one for affray and assault on police, two for public order offences, one for assault causing actual bodily harm and possession of class A drugs, one for a racially aggravated public order offence, one for ticket touting, one for possession of class A drugs, one for theft and possession of an offensive weapon, and one for breach of a banning order.

"A number of lines of inquiry are being pursued," said a police spokesman. "There will be a significant post-match review and further investigation will take place to identify those responsible for committing offences."

The Football Association has been criticised for staging the semi-final at 5.15pm, allowing supporters to start drinking alcohol well before kick-off. However, the game in Newcastle kicked off at noon.