"While I very much appreciate PM Abe going to Iran to meet with Ayatollah Ali Khamenei, I personally feel that it is too soon to even think about making a deal. They are not ready, and neither are we!" Trump tweeted.
This comes hours after two oil tankers were attacked in the Gulf of Oman, raising tensions in the region.
Abe has just completed his two-day visit to Iran, becoming the first sitting Japanese premier to visit the country since its 1979 Islamic Revolution. While talking to reporters, Abe on Wednesday said that helping to ease tension in the region was "the one single thought that brought me to Iran", reported Al Jazeera.
The United States has blamed Iran for the recent attack.
"The attack on two oil tankers on June 13 was one in a list of Iranian and Iranian-backed attacks over the last month. It was a clear threat to peace, security and freedom of navigation," US Secretary of State Mike Pompeo said during a media briefing.
"The US will defend its force, interests, partners and allies. We call upon all nations threatened to join us in that endeavour," he added.
Tensions have escalated in the already simmering region. The US and Iran are at loggerheads since President Donald Trump's decision in May 2018 to withdraw from a landmark nuclear deal.
Following this, the US slapped a multitude of sanctions on Iran, citing the latter's support to state-sponsored terrorism and conflicts.
The historic 2015 deal between Iran and world powers including the EU and the US, offered sanctions relief to Iran for scaling back its nuclear programme.
The US has remained rooted to its stand, saying it would continue to "impose maximum pressure" against Iran till the regime gives up its "destabilising ambitions" of expanding its nuclear programme.
Washington recently announced that no fresh sanction waivers will be issued for Iranian oil imports to eight countries, including India.