The aid groups, including the World Health Organisation and UN agencies, said more than one-fifth of sick Palestinians who needed to leave the territory for treatment in Israel had either been refused or had their applications delayed. The groups called on Israel and Egypt to open the border crossings with Gaza.
Max Gaylard, the UN humanitarian co-ordinator for the Palestinian territories, said the blockade undermined the local healthcare system and put lives at risk.
"It is causing ongoing deterioration in the social, economic and environmental determinants of health," he said.
"It is hampering the provision of medical supplies and the training of health staff, and it is preventing patients with serious medical conditions from getting timely specialised treatment."
The agencies highlighted the case of a student, Fidaa Hijji, who died of cancer while waiting for Israeli permission to go to hospital for a bone marrow operation.
Repeated applications to cross the border were ignored even though Hijji, who was 18 when her cancer was diagnosed in 2007, had confirmed medical appointments.
Permission for her entry to Israel was finally given a day after she died last month.
Israel generally permits supplies of drugs into Gaza, but not always of enough to prevent shortages. Certain medical equipment, such as x-ray and electronic devices, is difficult to bring in and clinical staff frequently lack equipment they need, the UN said.
The blockade was imposed after Hamas militants seized control of Gaza in 2007.
Health professionals in Gaza have been cut off from the outside world, with few doctors, nurses or technicians able to leave for the training necessary to update their clinical skills or learn about new medical technology during the past decade, the agencies said.
Many specialised treatments, such as heart surgery and some cancer treatments, are unavailable in Gaza.
"An effective healthcare system cannot be sustained in isolation from the international community," Tony Laurance, the WHO head in the West Bank and Gaza, said.
"Open borders are needed to ensure the health of the 1.4 million people in Gaza."
WHO figures indicate that 21% of the 1,103 applications last month to travel to Israel for hospital appointments were denied or delayed.
Twenty-nine patients died last year awaiting referral, down from 46 in 2008.
An Israeli spokesman said approvals had increased by 25% since 2008.
"Not only are we doing our utmost to allow the people of Gaza every possible medical treatment, but we are doing this in a situation in which their own government is imposing a state of war and trying deliberately to harm Israelis, including those whose mission is to assist the very people of Gaza," Yigal Palmor, a spokesman for Israel's foreign ministry, said.