The coins were used in the last six months, bosses believe
The Mersey Tunnels have lost about £86,000 in revenue because of some motorists using fake £1 coins.
Operator Merseytravel contacted police to investigate after the fakes were found in its collection system.
The coins are suspected to have been used in the Queensway and Kingsway tunnels, which run beneath the River Mersey, for about six months.
Merseytravel promised action against the fraudsters and said it was looking at ways to tackle the problem.
Official figures from the Royal Mint suggest there are around 30m counterfeit £1 coins in circulation across the UK.
'Act of fraud'
Merseytravel said it believed the coin scam was a national, rather than local issue.
"Millions of people use the tunnels every year and 99.9% do so in the appropriate way," said a spokesman.
"Every time someone puts a fake £1 coin into the system - or into the Mersey Tunnels toll account - they are committing an act of fraud.
"But we are on to them.
"This is a massive nationwide problem, but something we picked up on locally and we are actively looking at ways we can tackle this, in discussion with Merseyside Police."