Some of the counter-demonstrators tried to grab officers' pistols while others threw stones and firecrackers.
The injured officer was hit by a firecracker. Police said they detained about five people.
Police forced Pro-Koeln to call off the rally because there were fears that more serious violence would take place, Burkhard Rick, a police spokesman, said.
Up to 3,000 policemen had been drafted in and part of the old city sealed off as authorities appealed for peaceful protests against a two-day congress called by the Pro-Koeln (For Cologne) group.
|Pro-Koeln activists oppose what they call 'Islamification' [AFP]
Pro-Koeln had hoped 1,500 people would attend Saturday's rally in the city centre to oppose the mosque and an "immigrant invasion" of Europe.
Those attending the congress, including like-minded leaders from Belgium, Austria and Italy, were protesting against "Islamification," and voicing support for Europe's "shared, thousand-year history" and "Western values and Christian traditions".
Fritz Schramma, Cologne's mayor whose city council gave the green light for the construction of the mosques, criticised Pro-Koeln as "arsonists and racists" hiding under the cloak of a "citizens' movement" in a speech earlier on Saturday.
An estimated 120,000 Muslims live in Cologne, widely viewed as one of Germany's most tolerant and well-integrated major cities.
By midday just 30 Pro-Koeln supporters had managed to reach the rally site, a marketplace near the city centre, as thousands of counter-demonstrators blocked streets leading to the square.
Some 5,000 more counter-demonstrators attended a peaceful rally nearby.
Saturday was the second day of the Pro-Koeln conference.
Opening events on Friday were severely hampered when hundreds of largely peaceful protesters managed to prevent the group's leaders from holding a news conference in a municipal building, forcing supporters of the groups to seek refuge on a rental boat cruising the Rhine River.
Eight people were arrested for throwing stones and paint balls at the boat.