Mikael Johannesson of the EPA says the government has not calculated how its proposal will affect the amount of traffic in Sweden and so it has failed to make an environmental impact assessment. Johannesson told Swedish Radio that this means the billion-krona plan is illegal.
Transport is responsible for about a third of greenhouse-gas emissions.
Other government bodies have criticised the transport plan. The Energy and Transport Agencies say the plans push Sweden's climate goal further out of reach.
A spokesperson for infrastructure minister, Catarina Elmsäter Svärd, declined to comment before the final version of the traffic plans is available.