"Al Jazeera condemns Israeli accusations against its journalists in Gaza and warns against (this) being a justification for targeting them," the network said in a statement.
The Israeli military published documents which it said it had found in Gaza that proved the men had a military affiliation to the groups. Reuters was not able to immediately verify the authenticity of the documents.
The Israeli military said the papers included Hamas and Islamic Jihad lists of personnel details, salaries and training courses, phone directories and injury reports.
"These documents serve as proof of the integration of Hamas fighters within the Qatari Al Jazeera media network," the military said.
Al Jazeera said that "The Network views these fabricated accusations as a blatant attempt to silence the few remaining journalists in the region, thereby obscuring the harsh realities of the war from audiences worldwide."
The Committee to Protect Journalists' Middle East programme said on X that the allegations amounted to the smearing of Palestinian journalists "with unsubstantiated 'terrorist' labels".
Israel has long accused Al Jazeera of being a Hamas mouthpiece and over the past year its authorities have ordered it to shut down its operations for security reasons, raided its offices and confiscated equipment.
Al Jazeera has said the Israeli actions against it were criminal, draconian and irresponsible and that the latest allegations were "part of a wider pattern of hostility" towards it.
The network says it has no affiliation with the groups and has accused Israeli forces of deliberately killing several of its journalists in the Gaza war, including Samer Abu Daqqa and Hamza AlDahdooh. Israel says it does not target journalists.
Qatar established Al Jazeera in 1996 and sees the network as a way to bolster its global profile.
Along with Egypt and the United States it has mediated ceasefire negotiations between Israel and Hamas, though the talks have been deadlocked for months.
