In a statement, the company said the use of the Toyota logo in Vote Leave campaign literature "could mislead the reader into thinking that Toyota endorses the Vote Leave campaign".
"We offer no such endorsement and further we are considering a formal legal complaint at this unauthorised use of our trademarks, which infringes our rights as the owners of the Toyota brand," it said.
Johan van Zyl, president and CEO of Toyota Motor Europe, said in February that the EU referendum was a matter for the British people, but said continued membership "is best for our operations and their long term competitiveness".
Some of the other companies named by Vote Leave -- Nissan, Vauxhall, which is part of General Motors, General Electric, Unilever and Airbus -- also cried foul.
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"We firmly support Britain remaining."
A spokesman for GE UK also told AFP that it had not given permission for its logo to be used, and said it had made its position clear in two public letters "supporting the UK's continued participation in the EU".
Nissan said it was not aligned to any political campaign, but a spokeswoman noted a statement from February saying that "the company believed it made the most sense for jobs, trade and costs for the UK to stay within Europe".