Natural England and APHA workers are striking in a dispute over pay, job losses and redundancy terms, following previous action in March.
In addition to the strike action, workers have been taking action short of a strike continuously since 16 March, including working to rule and an overtime ban.
It is part of the largest industrial action Prospect the union has taken in more than a decade.
The strike, which also includes workers from the Health and Safety Executive (HSE), follows refusal from government to enter talks to resolve the current pay dispute.
The government had imposed a pay control of 4.5%, with Prospect saying this would "further erode living standards, with inflation running at 10.1%."
"This leaves civil servants with some of the worst pay settlements in the public sector this yea," the union said, pointing to members’ pay falling by up to 26% since 2010 in real terms.
Prospect represents tens of thousands of specialist and technical staff in the Civil Service, including the Animal and Plant Health Agency (APHA) and Natural England.
They are among around 40 organisations where action is taking place.
Mike Clancy, general secretary of Prospect, said they were being "singled out by a government intent on leaving its own workers at the back of the pay queue".
“Why is this government treating its employees worse than anyone else in the public sector?" he asked.
“For months we have been pressing ministers to put forward a serious offer that recognises the cost-of-living crisis facing our members.
"But instead of coming to the negotiating table, the government has published a pay control of 4.5% for 2023-24 – with nothing on the table for last year.
“This industrial action was entirely avoidable, but the failure by government to make a comparable offer to elsewhere in the public sector has made it inevitable.”
Earlier this year, more than 300 call-centre workers at the Rural Payment Agency (RPA) held a strike over pay.
The PCS, which represents workers employed by government departments, had asked for a 10% pay increase, better job security and no slashes to redundancy terms.
