The deal signed with Canada means the two countries will continue to trade under the same rules as when the UK was an EU member state while they negotiate a "bespoke" agreement.
The Regional Comprehensive Economic Partnership (RCEP) signed by 15 countries encompasses around a third of world trading activity.
Japan is the UK's 11th largest export market with the value of trade between the two countries reaching £29 billion (€32 billion) in 2018.
Many major European exporters to Britain have sounded cries of alarm on the urgent need for a new post-Brexit free trade agreement.
The UK and the EU need to strike a deal on trade and future relations this year.
The EU’s chief negotiator Michel Barnier says the UK cannot have a Canada-style trade deal with the bloc, prompting an angry response from Downing Street.