Tokyo's moves aim to minimise Brexit's impact on Japanese companies as Britain negotiates its exit from the EU, the business daily Nikkei reported.
Prime Minister Shinzo Abe said he wants to reach a basic free trade agreement with the EU next month.
More than 1,000 Japanese companies operate in Britain, employing some 140,000 people in the country, while Japan's direct investment in the UK has topped 10 trillion yen ($96 billion) to date.
Japanese officials have already warned businesses with European headquarters based in Britain that they may have to relocate to continental Europe after a final deal is signed between London and the EU.
Japan's major automakers have so far backed the British economy, with Toyota announcing a £240 million investment in a car assembly plant while Nissan gave the green light to new investments at its plant in northeast England.
The announcements raised questions about what assurances they had been offered by the British government.
Japan is planning to start informal talks with Britain while it remains in the EU, but will wait until the country has left the bloc before launching formal bilateral negotiations, the Nikkei report said, without citing sources.
"As (the UK) is not allowed to launch formal negotiations with a third country under the EU rules, the Japanese and British governments will prepare (informal) talks behind the scenes," it said.
Japan does not currently have a trade deal with the European Union but is locked in long-running negotiations with the bloc. On Saturday, Abe said he is aiming to reach a Japan-EU free trade deal during his visit to Germany to attend a Group of 20 summit.
"I hope to hold a summit meeting with the EU and reach a basic agreement there," he said in a televised speech in western Japan's Kobe.
"The Japan-EU Economic Partnership Agreement will be a model for 21st century economic order," said Abe.
He added that he hoped the EU deal would provide the same stability promised by the enormous Trans-Pacific Partnership pact. US President Donald Trump has pulled out of the TPP, effectively putting the deal on hold.
Britain stunned the EU when it voted to end its four-decade membership of the 28-nation bloc in a referendum last year.
But Prime Minister Theresa May's disastrous showing in elections on June 8, in which she lost her parliamentary majority, has sparked speculation that her Brexit plans may be watered down or even reversed.