"I wish to express my sorrow at the incidents that occurred during an illegal demonstration in Istanbul," Gul said on Monday.
"Everyone must abide by the law, but when they don't, the police must be very careful in the way they react."
Riot police chased, kicked and used truncheons to beat
protesters who had gathered for an unauthorised demonstration in Istanbul on Sunday.
Police also sprayed tear gas directly into protesters' faces and could be seen kicking a woman in the face.
"We were shocked by images of the police beating women and young people demonstrating in Istanbul," said a joint statement issued by Olli Rehn, the EU's commissioner for enlargement, Luxembourg's Foreign Minister Jean Asselborn and Britain's Europe Minister Denis MacShane.
"On the eve of a visit by the EU during which the rights of women will be an important issue, we are concerned to see such disproportionate force used against demonstrators," they said.
Foreign Minister Gul: Police must
be very careful in its reaction
Luxembourg holds the rotating EU presidency, which Britain will take over this year. The meeting comes amid concerns about a slowdown in Turkey's progress towards improving democratic standards since December, when the bloc agreed to extend the membership talks with the mainly Muslim nation.
"It is extremely important that the momentum of the reforms are kept up," Rehn said in Ankara on Sunday.
The EU officials were expected to address Turkey's efforts to expand freedoms, curb torture and improve the rights of women and trade unions.
The EU leaders are expected to press Ankara to quickly sign a protocol that the EU says will amount to a de facto recognition of Cyprus, a new EU member whose government Turkey has refused to recognise.
The EU says signing a customs protocol with Cyprus and the other new EU members is a requirement for Turkey to start EU membership talks in October.
Gul on Sunday pledged to sign it on time and said Turkey was determined to press ahead with other reforms.
On Monday, Human Rights Watch released a report expressing concern that the government was not doing enough to ensure the return of hundreds of thousands of Turkish Kurds who were displaced amid intense fighting between Turkey's military and autonomy-seeking Kurdish rebels.
"Turkey still has much to do on the protection of freedom of expression, freedom of religion, language rights and protection against torture," the group added in a statement.
Monday's talks are also expected to address the Middle East peace process, Iran, Iraq, the Caucasus and EU-Nato relations.