California's attempts to cut its carbon emissions through legislative measures received a dual blow last week after planned rules governing emissions from cars and ships met with fresh legal obstacles.

As anticipated, the Environmental Protection Agency (EPA) last Friday made good on its threat to block a planned state law that would force automakers to produce cars with significantly higher fuel efficiency from next year.

The proposed rules were made under the Federal Clean Air act, which allows California to set more stringent air pollution rules to cope with its exceptional levels of smog. Advocates of the new standards, which have secured support from 18 other states which plan to adopt the same standards, said that they would cut automotive emissions by 40 per cent by 2020.

However, a waiver from the EPA is required for California to set different standards to the rest of the country and despite granting over 50 such waivers in the past, last December the federal agency said it would reject California's latest proposals.

In a regulatory notice issued last Friday, administrator Stephen Johnson confirmed that the EPA would not grant a waiver, ruling that while "the conditions related to global climate change in California are substantial, they are not sufficiently different from conditions in the nation as a whole to justify separate state standards".

The EPA maintains that new federal standards agreed last year and designed to cut automotive emissions by 31 per cent by 2020 make separate state regulations unnecessary.

The fate of the proposed standards now rest with the courts following California's announcement in January that it is to join forces with a number of states and environmental groups to sue the EPA over its refusal to grant a waiver.

David Doniger, policy director of the National Resources Defense Council's Climate Center and the lead attorney for the organisation's waiver litigation efforts, argued that the EPA's ruling that California did not face a unique global warming threat was "factually and legally wrong".

"No other state can claim the same wide range of severe impacts that California will suffer – indeed, already is suffering – more illnesses from heat-enhanced smog levels, dramatic reductions in state's water supply, more horrendous wildfires, sea level rise and agricultural losses," he said.

According to EPA documents released by Congress in January, the agency itself has little confidence that it can block the new rules in court, with staff concluding it would probably lose any legal case.

The EPA ruling comes as Californian attempts to use the Clean Air Act to also tackle emissions from ships and ports also suffered a blow after a San Francisco court ruled it would need a separate waiver from the EPA before imposing pollution limits on cargo ships, cruise ships and other marine vessels that visit the state's ports.

The California Air Resources Board has stopped enforcing the rule, which was implemented last year and targets the use of auxiliary diesel engines within 24 nautical miles of the coast, and is now considering whether to appeal the decision to the Supreme Court or seek a waiver from the EPA.

However, despite the setback, officials remained confident that emissions limits would ultimately be placed upon the shipping sector. "This is critical to protecting public health, particularly around ports," air board spokeswoman Gennet Paauwe told the Los Angeles Times. "It is part of our large plan to cut emissions, particularly for the ports and goods-movement sectors."