Chief Superintendent Rob Nixon said there were 1,000 EDL supporters and 700 others backing a counter protest organised by Leicester Unite Against Fascism.
Mr Nixon blamed a hardcore element of the EDL which was determined to break through police lines.
He said an investigation was ongoing. The UAF counter-protest passed without incident.
Before they were rounded up by police a group of EDL supporters attacked the Big John's fast food restaurant, in Humberstone Road.
Usman Ali, area manager for the chain, said: "They smashed four windows and came inside the shop and frightened our customers.
"Everyone is fine, although it was a very frightening experience for our staff and the people who were here eating their dinner."
Witness Imtiaz Noor Mohammed, 21, of North Evington, said: "I was with friends getting something to eat.
"People saw them coming and someone locked the door. They smashed some windows and one of the EDL people kicked the door open and stood there threatening people.
"There were only families in there; men, women and children eating together. The whole thing was over in a minute but it was very scary."
The EDL appeared to have failed to stick to an agreement with police for its supporters travelling by coach to rendezvous with police at Leicester Forest East service station on the M1 before being escorted into the city centre. Instead, around 400 of its followers appeared without warning in Market Harborough. Police said they diverted officers to the town quickly.
Youtube footage of incidents, including the one at Big John's, is at:
www.thisisleicestershire.co.uk
