Merkel backed Abe's comments, urging negotiators to "do it quickly" and then slammed the EU for its slow decision-making process.
"Decision making in the EU is sluggish … it's not a blame game and I get often it's the individual member states … Often they can't agree," Merkel said.
Japan is the EU's sixth-largest trading partner behind the likes of China and Russia, and last year accounted for around 124.5 billion euros (about US$133.7 billion) of trade.
The comments from Abe and Merkel come following meetings with U.S. President Donald Trump who has continuously taken an anti-globalization stance. Trump has accused Japan of purposefully devaluing its currency to boost its exports, a charge that Abe has denied. The U.S. president has also withdrawn from the Trans-Pacific Partnership, a major trade deal that included Japan. Trump's agenda has put more emphasis now on a free trade pact with the EU.
Trump's advisor Peter Navarro, who heads up the National Trade Council, also accused Germany of using the weak euro to boost exports. Against this backdrop, Merkel warned against putting up barriers between countries.
"It's very good that Japan says we want a free trade agreement ... Germany would love to be a propelling driver behind the agreement coming into being. We do want open markets … we certainly don't want any barriers … we want to link our societies with one another and let them deal fairly with one another and that is what free trade is all about," Merkel said.
Abe framed his comments around the need for connectedness among countries, just as technology increasingly is becoming connected. Talking about the internet of things (IOT) — the billions of internet-connected devices expected to come online in the next few years — Abe said that Germany and Japan need to work together to drive innovation.
The Japanese prime minister called for "common technology standards" across the world to help this. "IOT will connect everything," Abe said.
He added: "It is through connectedness that economies will grow, Japan having grown through reaping … the benefits of free trade and investment, wants to be the champion upholding open systems alongside Germany."