Violence broke out close to the city`s Alte Oper concert hall hours before the ECB building`s official opening.
"Blockupy" activists are expected to attend a rally later on Wednesday.
In earlier disturbances, police in riot gear used water cannon to clear hundreds of anti-capitalist protesters from the streets around the new ECB headquarters.
Organisers were bringing a left-wing alliance of protesters from across Germany and the rest of Europe to voice their anger at the ECB`s role in austerity measures in EU member states, most recently Greece.
The bank, in charge of managing the euro, is also responsible for framing eurozone policy and, along with the IMF and European Commission is part of a troika which has set conditions for bailouts in Ireland, Greece, Portugal and Cyprus.
A spokesman for the Blockupy movement said the troika was responsible for austerity measures which have pushed many into poverty.
Police set up a cordon of barbed wire outside the bank`s new 185m (600ft) double-tower skyscraper, next to the River Main.
But hopes of a peaceful rally were dashed as clashes began early on Wednesday.
Tyres and rubbish bins were set alight and police responded with water cannon as firefighters complained they were unable to get to the fires to put them out. One fire engine appeared to have had its windscreen broken.
Activists said many protesters had been hurt by police batons, water cannon and by pepper spray.
Police said as many as 80 of their officers had been affected by pepper spray or an acidic liquid. Eight suffered injuries from stone-throwing protesters.
Police spokeswoman Claudia Rogalski spoke of an "aggressive atmosphere" and the Frankfurt force tweeted images of a police van being attacked. They were braced for further violence as increasing numbers of activists arrived for the rally.
Blockupy accused police of using kettling tactics to cordon off hundreds of protesters and appealed for supporters to press for their release.
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