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.
Two France 24 journalists who were there to interview Mada Masr's chief editor Lina Attallah were also arrested on the premises.