KYIV, Ukraine — President Volodymyr Zelensky of Ukraine called for the nation’s largest and oldest branch of Christian Orthodoxy to be outlawed as long as it continues to answer to church leaders in Moscow, proposing a new law that he said would ensure the nation will “never allow anyone to build an empire inside the Ukrainian soul.”

The law, if enacted, would further strain a centuries-old spiritual relationship between Russia and Ukraine, codifying the already deep rift in the Eastern Orthodox church.

Kyiv has long worried that Russia is using the Ukrainian Orthodox Church of the Moscow Patriarchate to provide cover for a network of clandestine agents whose goal is to undermine Ukraine from within. Over the past month, Ukrainian security agencies have engaged in a series of raids of monasteries and religious institutions hunting for saboteurs among the clerics.

The Security Service of Ukraine, known as the SBU, has interrogated dozens of religious leaders, administering polygraph tests to some, and claimed to have found “literature that denies the existence of the Ukrainian people, its language, as well as the very right of Ukraine to statehood.” After raids last month, the church called the accusations of collaboration between its clergy and Russia “unproven and groundless.”

As of last month, 33 priests had been arrested for assisting Russia since the invasion began in February, according to the Ukrainian authorities. Most of them were charged with gathering intelligence for Moscow’s forces.

There are two rival Orthodox churches in Ukraine — the Orthodox Church of Ukraine, which takes its orders from Kyiv, and the Ukrainian Orthodox Church of the Moscow Patriarchate.

The recent raids and suspicion involve the latter, which is subordinate to the Russian Orthodox Church and Patriarch Kirill, who has strong ties to President Vladimir V. Putin and has been outspoken in his support of the invasion.

It had more than 10,000 parishes across the nation in January, before the war, according to a group that tracks the movement of parishes. The branch has declared its independence from Moscow but still formally takes orders from Russia. It has condemned the war, but that has not been enough to allay concerns among Ukrainian security services.

In a speech to the nation late Thursday, Mr. Zelensky proposed a law “making it impossible for religious organizations affiliated with centers of influence in the Russian Federation to operate in Ukraine.”

“We will ensure, in particular, spiritual independence,” Mr. Zelensky said, noting that the law was needed to ensure that Russia cannot “manipulate Ukrainians and weaken Ukraine from within.”

The Ukrainian Parliament has two months to consider the law and experts noted it could face challenges in court.

The religious history of Ukraine and Russia is deeply intertwined. Orthodox Christians in both Russia and Ukraine trace their faith back to the conversion in 988 of the Grand Prince of Kyiv — known as Vladimir by Russians and Volodymyr by Ukrainians.

After the pagan grand prince was baptized by missionaries from Constantinople, the capital of the Byzantine Empire, Kyiv became the most important religious center for the people known as the Slavs. After Kyiv was sacked by the Mongols in the 13th century, it fell into decline. By 1686, Russia had conquered eastern Ukraine and Kyiv and the Orthodox church became subordinate to Moscow.

Efforts by Ukrainian Orthodox Christians to create their own church and break from Moscow were tied to independence movements in 1921, 1942 and 1992. Those efforts largely failed.

But after Russia illegally annexed Crimea in 2014 and fomented war in the east, the main spiritual guide for Eastern Orthodoxy, Patriarch Bartholomew of Constantinople, granted the Kyiv branch independence.

That move led Moscow to cut ties with Bartholomew. The Ukrainian Orthodox Church of the Kyiv Patriarchate now includes more than 7,000 parishes.