"We, of course, want to continue to have a strong relationship with Israel," she said.
The EU's decision on the ban, announced in July, marked a new international show of displeasure with Israeli settlements built on lands captured in the 1967 Mideast war.
The Palestinians claim some of those territories — the West Bank, Gaza Strip and east Jerusalem — for their hoped-for state.
The EU ban applies to grants, prizes and financial instruments and that the new funding guidelines go into effect in 2014. The EU issues dozens of grants, totaling millions of euros, to Israeli universities, companies and researchers every year.
From Paris, Kerry was scheduled to hold talks in London with Palestinian President Mahmoud Abbas and British Foreign Secretary William Hague before returning to Washington.
Associated Press writers Raf Casert in Vilnius, Lithuania, and Sarah DiLorenzo contributed to this report.
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