The stoppages are part of a series of demonstrations by public sector employees against Macron, who has pledged to reduce public spending, trim jobs and overhaul large parts of the vast French state.
All unions representing civil servants have backed Tuesday's strike, a rare show of unity which was last seen around 10 years ago.
Their walk-out, which will affect schools, public kindergartens, flights and some energy infrastructure, is the third stoppage since Macron's election in May 2017.
"Thanks to the civil service, all of the unions in this country will be together," said labour leader Bernadette Groison from the FSU union. "That shows how high the stakes are."
The centrist government plans public sector reforms next year which would lead to the greater use of contract workers for some state services and a cut of 120,000 jobs by 2022 out of 5.6 million.
Many civil servants fear that the government plans to scrap their special status and job-for-life privileges, a measure that has already been announced for new recruits on the state railways, the SNCF.
That move on the railways, though generally supported by the French public, has sparked one of the longest strike sequences ever on the network which began at the beginning of April.
Workers have been downing tools every two days out of five since 3 April and will begin a new round of stoppages on Tuesday which has seen high-speed services and commuter trains badly affected.
But Macron has vowed to be uncompromising and promised to deliver on his rail reform promise and cuts to France's public spending, which was part of his election manifesto.
France has one of the biggest public sectors in Europe relative to the size of its economy and the country has not balanced its budget since the 1970s, leading to a public debt equivalent to nearly 100 percent of GDP.
But unions accuse Macron of wanting to destroy public services which are a vital source of employment and a pillar of communal life in many areas of the country.
Around 130-140 demonstrations have been organised by civil servants on Tuesday with unions hoping turnout will be higher than the last day of action on 22 March when an estimated 300,000 gathered nationwide.