The comments from Fumio Kishida Thursday come after four years of talks aimed at hammering out a free-trade agreement, with negotiators working toward signing a deal at a G20 meeting in Hamburg next week.
Clinching a deal would be a victory for free-trade advocates after US president Donald Trump pulled the United States out of the Trans-Pacific Partnership this year, dealing a possibly fatal blow to the mooted 12-nation deal.
EU Trade Commissioner Cecilia Malmstrom and agriculture commissioner Phil Hogan will visit the Japanese capital from Friday, Kishida said.
"I think they're going to be very tough and difficult negotiations," Kishida added.
"It's not yet decided when we'll reach a conclusion or how long we'll be negotiating.
"We'd like to make the maximum use out of the time we've got."
A European source told AFP that Malmstrom and Hogan's visit suggests there are still some political issues to work through.
"If they're going to Tokyo it's an important signal" but it doesn't mean a deal is imminent, the source added.
Brussels wants Japan to eliminate its 30 percent tariffs on some EU-made cheese, while Tokyo wants duties cut on cars which it exports to the 28-member bloc.
Any deal they reach would cover some 28 percent of global GDP.
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