The MacArthur Foundation, a US NGO that supports academic and human rights initiatives, will shut down its activities in Russia after lawmakers included it on a “patriotic stop list” of foreign groups.

Russia’s upper house of parliament asked the prosecutor general’s office, foreign ministry and justice ministry earlier this month to investigate whether the MacArthur Foundation and other NGOs should be declared “undesirable” under a new law that would ban them in Russia.

The 12 organisations listed on the stop list also included business magnate George Soros’s Open Society Foundations and the US pro-democracy NGO Freedom House, as well as Polish and Ukrainian non-profits.

In a statement, the MacArthur Foundation said comments by legislators and inclusion on the stop list “make it clear that the Russian government regards MacArthur’s continued presence as unwelcome”.

“The recent passage and implementation of several laws in Russia make it all but impossible for international foundations to operate effectively and support worthy civil society organisations in that country,” it said.

Since opening in Russia in 1992, the MacArthur Foundation has given out grants worth more than $173m (£110m) in the country. Scientists, educators and human rights advocates lamented the announcement that it would leave.

Viktor Voronkov, director of the Centre for Independent Sociol Research, which received a grant from the MacArthur Foundation in 2012, said the fund was “not driven by political motives” and had been the “main partner for Russian science” after the Soros Foundation reduced its funding in the area.

Yelena Topoleva-Soldunova, a member of the presidential human rights council, said the foundation’s closure would be a “pretty grievous loss” especially for universities in the regions that had been its focus. “Our economic situation is not very easy right now and … there are not so many Russian sources of support,” she told state news agency RIA Novosti.

A spokesman for the Russian president, Vladimir Putin, declined to comment on the closure.

Passed in May, the law against so-called undesirable organisations is the latest step in a broader crackdown on NGOs, which Putin claimed in March were often used by western intelligence agencies to “discredit the authorities and destabilise the internal situation in Russia”. Lawmakers have also proposed that groups including Human Rights Watch, Amnesty International, Carnegie Moscow Center and Memorial, Russia’s oldest human rights organisation, be banned as undesirable.

Since 2012, a law on “foreign agents” has effectively branded as spies all NGOs that receive overseas grants for allegedly political activities and subjected them to audits. But locally backed organisations have also suffered: earlier this month, Russian telecoms magnate Dmitry Zimin was forced to close his Dynasty Foundation, which supported science education and research and was funded through offshore accounts, after it was deemed a foreign agent.

In addition, at least half a dozen western academics have been fined or expelled from Russia over visa issues in the past year. Earlier this month, American investment consultant Kendrick White was fired from his post promoting innovation at a university in Nizhny Novgorod.

On Wednesday, a court fined the NGO Perm-36, which ran Russia’s only fully preserved Soviet-era gulag camp until local officials seized control of it this year, 300,000 roubles (£3,400) and its director 100,000 roubles (£1,120) for failing to register as a foreign agent. Later, Perm-36 said it had filed court papers to challenge its inclusion on the foreign agents list.

On Tuesday, the justice ministry issued a warning to 12 NGOs included on the state register of foreign agents, including many of Russia’s best-known human rights and environmental organisations. The ministry said they were in violation of the law’s stipulation that registered groups note they are a foreign agent on all their materials and publications, and that they could be fined 500,000 roubles (£5,600).