Two activists, Saif Abu Keshek from Spain and Thiago Avila from Brazil, were detained by Israeli authorities late on Wednesday and brought to Israel.
Their lawyer, Hadeel Abu Salih, said that their arrest was unlawful due to a lack of jurisdiction and that the mission was meant to provide aid to civilians in Gaza, not to any militant group.
The activists were part of a second Global Sumud flotilla, launched in an attempt to break Israel's blockade of Gaza by delivering humanitarian assistance.
More than 100 other pro-Palestinian activists aboard the boats were taken to the Greek island of Crete.
A court spokesperson confirmed that their remand had been extended until May 5.
The governments of Spain and Brazil issued a joint statement on Friday calling their detention illegal.
Israeli authorities requested a four-day extension of their arrest on suspicion of offences that include assisting the enemy during wartime, contact with a foreign agent, membership in and providing services to a terrorist organisation, and the transfer of property for a terrorist organisation.
The activists deny the allegations and claim they were subjected to violence en route to Israel and kept handcuffed and blindfolded until Thursday morning.
The Israeli military has referred to the incident as violent physical obstruction by Abu Keshek and Avila, but their lawyer disputes this account.
The detention of pro-Palestinian activists raises questions about freedom of speech and the right to protest.
