Mr Gove said town halls should prioritise "improving road layouts and junctions to optimise traffic flow, for example by considering removal of road humps".
The instruction is part of Government efforts to reduce air pollution, which could also see owners of diesel vehicles hit with a new tax.
Ministers say they want councils to use other methods, such as changing road layouts, before introducing new charges on drivers.
The 98-page document, published by the Department for Environment, Food and Rural Affairs, outlined plans for reducing roadside levels of nitrogen dioxide, which have soared in recent years.
Many cities in the UK now breach legal pollution limits, and tens of thousands of deaths each year are linked to air pollution.
Speed bumps are said to double emissions by causing vehicles to repeatedly slow down and speed up. Research by scientists at Imperial College London showed a diesel car emits 98 per cent more nitrogen dioxide when driving over speed bumps compared to narrower and shallower “road cushions”.
Emergency services have said speed bumps can also delay ambulances, fire engines and police cars responding to urgent calls.
Road safety campaigners, however, say the bumps are crucial in slowing cars down in residential areas, including near schools, and therefore save lives.
Kevin Clinton, head of road safety at the Royal Society for the Prevention of Accidents, said: ‘Removing speed humps, which are proven to be an effective way of reducing road casualties, would increase risk to all road users, but especially to pedestrians, pedal cyclists and children, and are one of the key reasons why death and injury on our roads have fallen so substantially over the last few decades.”
The new plan was released after the High Court ruled the Government is breaking the law by not doing more to reduce air pollution.
The strategy will allow local councils to impose a levy on owners of diesel vehicles using busy roads and ban them from some roads during peak hours.
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