Three Egyptian news editors from local news outlet Mada Masr have been referred for prosecution after plainclothes police raided its office on Sunday, the site said.
"We have just got our phones and laptops back. Security forces left. Lina Attalah, Mohamed Hamama and Rana Mamdouh have been taken to the prosecution service, according to one of the men who entered our offices," the independent news site said.
It posted on social media that nine plain-clothed officers questioned the journalists on site for several hours, demanding that they unlock their phones and laptops and hand them over.
The whereabouts of the three who were detained is not yet known.
Sunday's raid came at around 1:30 pm (11:30 GMT), a day after Shady Zalat, 37, a news editor who has worked at the prominent website since 2014, was arrested at his home.
The news website's Twitter feed said Zalat was released later on Sunday at around 5:30 pm ((15:30 GMT).
Mada Masr publishes investigations into corruption and security issues in both Arabic and English.
It published a controversial article last week alleging that President Abdel-Fattah al-Sisi's son Mahmoud would be transferred to Moscow on a diplomatic posting.
His reassignment from a senior intelligence post in Egypt came after he had been criticised within the security apparatus, Mada Masr reported.
The article, citing unnamed Emirati and Egyptian officials, gave details about the country's security agencies at a time when press freedoms are shrinking in the Arab world's most populous nation.
AFP approached the interior ministry for a comment to no avail.
A Mada Masr journalist, speaking from outside the news site's building, told AFP on Sunday that police officers were still inside.
He described seeing several vehicles belonging to the security forces and was met by plainclothes police officers at the entrance of the building.
"They initially prevented me from entering then they took me up to the sixth floor, where the office is. We knocked on the door and I saw my colleagues for a fraction of a second," he said.
"A policeman, also plain-clothed, said we don't want anyone coming or going and I was let go," he added.
Foreign journalists held
Two France 24 journalists who were there to interview Mada Masr's chief editor Lina Attallah were also arrested on the premises.
"We asked why we were detained but no one answered," Eric de Lavarene, one of the France 24 reporters, told AFP. He said that he had had time to alert the French embassy of his arrest.
They were released with other Mada journalists after security forces left the premises.
Lawyers gathered outside the building were denied entry to speak with the journalists.
Rights group Amnesty International condemned Sunday's raid and called on the government to "refrain from punishing journalists for doing their legitimate work".
Egypt jails more journalists than any other country behind China and Turkey, according to the New York-based watchdog Committee to Protect Journalists.
Mada Masr is one of hundreds of websites blocked by Egyptian authorities in recent years. It can be accessed domestically only via a virtual private network (VPN) app.