The state-run Herald paper tweeted that Evan Mawarire was also being charged with disturbing the peace.
According to BBC, activists organised a "stay-at-home" protest last Wednesday and planned similar shutdowns this week.
It has mostly been organised on social media and WhatsApp using #ThisFlag.
Zimbabwe's economic crisis has worsened recently, leading to a chronic cash shortage and delays paying civil servants. BBC reports.
Pastor Mawarire was summoned for questioning by police ahead of a two-day "stay-at-home" protest called for Wednesday and Thursday.
The preacher recorded a video saying: "You are watching this video because I have either been arrested or have been abducted. It's a video we had pre-recorded for a day like this one."
He ended his message saying that he hopes the shutdowns have been successful.
"Hold this government to account. Never let them get away with anything," he said.
Authorities have been trying to trace who has been sending out messages about the national shutdown, as several activist groups have been involved. BBC reports.
Last Wednesday's stay away led to a complete shutdown of schools, businesses and shops across the country.
It was the biggest strike action since 2005 and public transport and some government departments, including the courts, also ceased to function.
According to BBC reports, last week, taxi drivers complaining about police extortion also clashed with the security forces in parts of Harare.
Civil servants who had not received their June salaries were paid in the wake of the strike.
These have to be paid in foreign currency as Zimbabwe abandoned its own currency in 2009 in order to stem runaway inflation.
There is also anger at a government ban on importing many goods which has been implemented in order to save scarce foreign currency.
However with unemployment at more than 90%, many Zimbabweans rely on cross-border trading to make a living.