The visit to the University of Wales in Aberystwyth was halted five minutes before the Queen was due to open a science-centre campus.
About 200 Welsh-language students and members of the Welsh Language Society mounted a protest near the building as 50 police struggled to keep them back from the approach road.
With minutes to go before the Queen's motorcade was due, three men burst through the cordon and ran down an embankment, pursued by officers. A policeman's helmet was knocked off and a placard was thrown from the crowd.
A quarter of a mile away, at the National Library of Wales, the Queen was preparing to get into her car for the short drive to the Centre for Glaciology.
But her personal-protection officer and the Dyfed-Powys Assistant Chief Constable, Keith Turner, hearing of the disturbance, advised her to cancel the final engagement of the five-hour tour.
Earlier, six students were arrested in connection with public-order offences and a seventh over criminal damage. Four of the men leapt over security barriers and ran towards the Queen's car, although they were stopped before reaching it.
The Queen appeared unaffected and continued waving to crowds further along the route.
Dyfed-Powys police said the inability to complete the tour was "very much regretted but the decision was not taken lightly". A Buckingham Palace spokeswoman said cutting short a visit by the Queen in this way was "certainly unusual" but it could not be said with certainty whether or not there were precedents in Britain.
"There have been a few occasions abroad when walkabouts have had to be cancelled on police advice because the crowd was getting too enthusiastic," she said.Reuse content