American influence in culture, science and education around the world took a high-profile blow on Friday after the US automatically lost voting rights at Unesco after missing a crucial deadline to repay its debt to the world's cultural agency.

The US has not paid its dues to the Paris-based UN Educational, Scientific and Cultural Organisation in protest over the decision by world governments to make Palestine a Unesco member in 2011. Israel suspended its dues at the same time and also lost voting rights on Friday.

Under Unesco rules, the US had until Friday morning to resume funding or explain itself, or automatically lose its vote. A Unesco official, who was not authorised to speak publicly about the issue, said nothing was received from either the US or Israel.

The suspension of US contributions, which accounted for $80m a year – 22% of Unesco's overall budget – brought the agency to the brink of a financial crisis and forced it to cut or scale back US-led initiatives such as Holocaust education and tsunami research.

Many in Washington are worried that the US will become a toothless Unesco member with a weakened voice in international programmes fighting extremism through education and promoting gender equality and press freedoms.

Some fear that a weaker US presence will lead to growing anti-Israeli sentiment within Unesco, where Arab-led criticism of Israel for territorial reasons has long been an issue.

"We won't be able to have the same clout," said Phyllis Magrab, the Washington-based US national commissioner for Unesco. "In effect, we [now won't] have a full tool box. We're missing our hammer."

The Unesco tension has prompted fresh criticism of US laws that force an automatic funding cutoff for any UN agency with Palestine as a member. The official list of countries that lose their votes was expected to be read aloud on Saturday before the entire Unesco general conference.

Israel's ambassador to Unesco, Nimrod Barkan, told the Associated Press that his country supported the US decision "objecting to the politicisation of Unesco, or any international organisation, with the accession of a non-existing country like Palestine".

Unesco is probably best known for its programme to protect the cultures of the world via its heritage sites, which include the Statue of Liberty and Timbuktu in Mali. But its core mission, as conceived by the US, a co-founder of the agency in 1946, was to be an anti-extremist organisation. It tackles foreign policy issues such as access to clean water, teaches girls to read, works to eradicate poverty, promotes freedom of expression and gives people creative thinking skills to resist violent extremism.

Among Unesco programmes already slashed because of funding shortages is one in Iraq that was intended to help restore water facilities. Also in danger was a Holocaust and genocide awareness programme in Africa to teach about non-violence, non-discrimination and ethnic tolerance, using the example of the mass killing of Jews during the second world war.

This loss is a particular blow to the US, since Holocaust awareness was one of the areas the country aggressively promoted in the agency's agenda when it rejoined in 2002 after an 18-year hiatus, during which the US had withdrawn from the organisation over differences in vision.

The Palestinian ambassador to Unesco, Elias Sanbar, said other countries were beginning to make up for the US shortfall.

"Is this in the interest of the US, to be replaced?" he asked.

The Unesco director general, Irina Bokova, lamented the change. "I regret to say that I'm seeing, in these last two years … a declining American influence and American involvement," Bokova said.

"I can't imagine how we could disengage with the United States at Unesco. We are so intertwined with our message. What I regret is that this decision became so divisive and triggered this suspension of the funding," she added.

Bokova said she accepted political reality and would find ways for Unesco to continue its work, despite a 2014 budget that is down by an estimated $150m.

Some worry about more serious consequences if Palestine joins other agencies such as the World Health Organisation.