Saif Abu Keshek, a Spanish citizen, and Brazilian Thiago Avila were detained by Israeli authorities last Wednesday and brought to Israel while more than 100 other pro-Palestinian activists on the boats were taken to the Greek island of Crete.
Abu Keshek and Avila's detention had initially been extended until Tuesday but the Ashkelon Magistrate's Court extended it further until May 10.
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.
The ships set sail from Barcelona on April 12.
Court documents show that Israel accuses Abu Keshek and Avila of offences including aiding the enemy, contact with a foreign agent and a terrorist organisation, prohibited activity involving a terrorist component and providing means to a terrorist organisation.
"I am convinced that there is reasonable suspicion," Judge Yaniv Ben-Haroush concluded after hearing parties' arguments in granting the extension.
Lawyers for human rights group Adalah had argued during the hearing that the allegations were baseless and there were no legal grounds for the continued detention of the two men.
They said no formal charges have been filed, and their detention was for purposes of ongoing interrogation.
Adalah said it would appeal the decision and would demand the immediate and unconditional release of Abu Keshek and Avila.
It also said the men had been tortured in custody - a charge dismissed by Israel.
Abu Keshek's wife, Sally Issa, told Reuters on Tuesday she had not been allowed to speak directly to her husband since his detention, relying instead on information from the Spanish consul and lawyers.
"They've told us that he's in good condition. He's hunger striking," Issa said.
"But he's okay. He suffered from torture on the boat when he was attacked by the Israelis."
Israel's foreign ministry has said that Abu Keshek and Avila are linked to Palestinian militant group Hamas, and that the flotilla "is another provocation designed to divert attention from Hamas' refusal to disarm".
A ministry spokesperson denied "false and baseless claims" of torture.
"Following violent physical obstruction by Saif Abu Keshek and Thiago Avila against Israeli staff members, staff were compelled to act in order to stop these actions. All measures taken were in accordance with the law," the spokesperson said.
Spanish Foreign Minister Jose Manuel Albares demanded Abu Keshek's immediate release, saying there was no evidence linking him to Hamas.
Albares said he had personally told his Israeli counterpart, Gideon Saar, that the activists' detention was illegal because Israel lacked jurisdiction in international waters.
Brazilian President Luiz Inacio Lula da Silva demanded Abu Keshek and Avila's release, saying the Brazilian's detention "is an unjustifiable action by the Israeli government, causes great concern, and must be condemned by all".
"The detention of the flotilla activists in international waters had already represented a serious affront to international law," Lula said.
Avila's spouse Lara Souza said her husband was on the sixth day of a hunger strike and was being monitored by doctors.
"He's better from the injuries but he is very weak, and the embassy is very worried about this," she said.
Due to the hunger strikes, the court ordered Israel's Prison Service to monitor the detainees' medical condition.
