The chief of the Russian General Staff has accused the United States of training former Islamic State fighters in Syria to try to destabilise the country.

General Valery Gerasimov’s allegations, made in a newspaper interview, centre on a US military base at Tanf, a strategic Syrian highway border crossing with Iraq in the south of the country.

Russia says the US base is illegal and that it and the area around it have become “a black hole” where militants operate unhindered.

Islamic State has this year lost almost all the territory it held in Syria and Iraq. Russian Foreign Minister Sergei Lavrov said on Wednesday the main part of the battle with Islamic State in Syria was over, according to the state-run RIA news agency.

The United States says the Tanf facility is a temporary base used to train partner forces to fight Islamic State. It has rejected similar Russian allegations in the past, saying Washington remains committed to killing off Islamic State and denying it safe havens.

But Gerasimov told the daily Komsomolskaya Pravda newspaper on Wednesday that the United States was training up fighters who were former Islamic State militants but who now call themselves the New Syrian Army or use other names.

He said Russia satellites and drones had spotted militant brigades at the US base. “They are in reality being trained there,” Gerasimov said, saying there were also a large number of militants and former Islamic State fighters at Shadadi, where he said there was also a US base.

“They are practically Islamic State,” he said. “But after they are worked with, they change their spots and take on another name. Their task is to destabilise the situation.”

Russia has partially withdrawn from Syria, but Gerasimov said the fact that Moscow was keeping an air base and naval facility there meant it was well placed to deal with pockets of instability if and when they arose.