The motion, put forward by the Welsh Conservatives was in response to the record-breaking petition against the new 20mph rules which has been signed by more than 443,000 people so far.
The petition has now been signed by the same number of people in Wales that voted for Mr Waters’ Welsh Labour Party at the last Senedd election.
Mr Waters was backed by members of his own party, as well as Senedd members from Plaid Cymru who have a power-sharing deal with Welsh Labour.
Mr Waters was also supported by the Welsh Liberal Democrat’s sole Senedd Member, Jane Dodds.
Commenting after the vote, Welsh Conservative Shadow Transport Minister, Natasha Asghar MS said: “It is completely inexcusable that Labour, Plaid and the Lib Dem have voted to support the Minister responsible for blanket 20mph speed limits, despite the the record-breaking Senedd petition calling for blanket 20mph speed limits to be scrapped.
“It’s clear, blanket 20mph speed limits are damaging livelihoods and jobs, will slow down emergency services, and cost the Welsh economy up to £9bn. That’s why the Deputy Minister’s position is untenable.
“Labour and Lee Waters will continue to carry on with their anti-motorist agenda. Only the Welsh Conservatives will continue holding the Labour Government to account, whist standing up for motorists.”
Mr Waters said that he understood that “lots of people are angry and frustrated”, saying that was listening to those that have signed the petition.
“We understand that not everybody likes this and we are willing to be flexible and how this is implemented in your local community,” he said.
He promised to “work with local authorities to help get it right” but said that “it was never going to be perfect on day one”.
Mr Waters added: “Speeds are already down and, as a result, we can expect to see fewer accidents, fewer casualties, fewer deaths, fewer tragedies, a little bit slower but a whole lot better.”
