By Peter Blackburn

BRUSSELS, Aug 17 (Reuter) - After a week of skirmishing on secondary issues, the European Union and Morocco started on Thursday to tackle the main problem of fish catch quotas but were still a long way from agreement.

The EU is seeking a new three-year agreement allowing mainly Spanish boats to return to Moroccòs rich Atlantic fishing grounds by next month.

"For the first time they got down to the substance of quotas with both sides showing flexibility," European Commission spokeswoman Sarah Lambert said.

During afternoon talks in closed session, both sides probed each other's negotiating positions.

But the European Commission, which represents the 15-member EU, has not yet made a formal quota offer, Lambert said. "We have work for several more days," she added.

An EU diplomat said Morocco rejected an informal offer earlier this week to cut fish catches.

Morocco is demanding sharp cuts in catches to protect threatened stocks and to allow its fishing industry to develop.

At the fifth round of talks in Rabat in June, Morocco sought a 65 percent cut in catches of octopus and squid and a 50 percent reduction in shrimp and hake trawling in northern Moroccan waters over three years.

It also wants EU vessels to land catches in Moroccan ports.

Fisheries Commissioner Emma Bonino told reporters on her return to Brussels on Wednesday that it was obvious the talks would be difficult but a deal by September was still the aim.

Bonino noted that the Spanish fishing fleet, the E s largest, must be reduced and that it was dangerous for it to depend so heavily on the Moroccan agreement.

Some 650 Spanish vessels have been tied up in port since the previous four-year accord was abruptly terminated one year early at the end of April.

Spanish fishermen, who were compensated by the Spanish government, have blockaded southern ports in recent weeks, halting imports of Moroccan fish into the EU and pressing for a quick resumption of fishing.