Turkey has been accused of cultural chauvinism and attempting to blackmail some of the world's most important museums in the wake of its demands for the return of thousands of archaeological treasures.

According to cultural chiefs in Berlin, Paris and New York, Turkey has threatened to bar foreign archaeologists from excavation sites in the country by not renewing their digging permits if governments refuse to return artefacts that Ankara says were unlawfully removed from Turkish soil. It has also threatened to halt the lending of its treasures to foreign museums, they say.

The government in Ankara, emboldened by the country's growing diplomatic and economic clout, has repeatedly said that the retrieval of the artefacts is part of a policy it intends to pursue for years, if necessary, calling it a "cultural war". However, it denies withholding permits as a form of leverage.

But the German Archaeological Institute, founded in 1829 and responsible for some of Turkey's most important excavation sites, says it has already felt the wrath of the Turkish authorities, after they threatened to withdraw excavation permits unless a huge 3,300-year-old Hittite sphinx was returned. When the sphinx arrived back in Turkey to much fanfare last year, permits for reconditioning and restoration work were renewed but those for digging remained outstanding.

Hermann Parzinger, president of the Prussian Cultural Heritage Foundation in Berlin, which among other collections oversees the city's Pergamon Museum, has accused Turkey of "playing a nasty game of politics" and of "threatening the future" of scientific work and other collaborations.

"The Turks are engaging in a rather aggressive style of politics," he said. "They are trying to blackmail us and others by pushing foreign archaeologists out. Their new tactic is to accuse us of not investing enough in the infrastructure of the digs."

Since the return of the sphinx – which Parzinger insists Germany did as a gesture of goodwill despite being under no legal obligation to do so – Turkey has demanded that three further objects be handed over by the Pergamon. They are the more than 2,000-year-old marble torso from the old fisherman statue found in Hadrianic baths of Aphrodisias, a medieval gravestone and parts of a 13th-century mihrab (prayer niche) from Konya. "All the artefacts were acquired legally more than a century ago and we are under no legal obligation to return them," Parzinger said.

Turkey is also in dispute with the Louvre in Paris, which has refused requests to return objects. Ankara retaliated two years ago with a ban on French archaeologists digging in Turkey.

Turkish officials are also at loggerheads with the Norbert Schimmel collection at the Metropolitan Museum of Art in New York over 18 objects they claim were illegally excavated, as well as with the British Museum in London over the Samsat Stele, a basalt slab from the 1st century BC.

Ankara says it only wants back what rightfully belongs to Turkey. Ertugrul Gunay, culture and tourism minister, said 4,067 artefacts were returned from 2002 to 2012. He said Ankara's demands coincided with a new-found pride in the country's cultural heritage.

"Our museum inventory is now on a par with that of European museums," he said recently.

"The times when we simply exhibited artefacts in cupboards is over. We have caught up … what we have taken back is only a very small part of what we will take back." He added that over the past five years, Turkey had "spent more on history" than any other European country.

Turkey is gearing itself up for the opening in 2023 – the centenary of the founding of the Turkish Republic – of the 2.5-hectare Museum of Civilisations in Ankara, which is due to showcase many of Turkey's best cultural treasures.

But archaeologists working in Turkey point to what they say is a sharp contradiction between the government's zealous attempts to retrieve artefacts, and its apparent negligence towards valuable excavation sites that are the talk of the archaeological world.

Among the most prominent is Allianoi, a Roman bath and spa complex in Izmir province, which was flooded in February 2011 on the orders of the government after the Yortanli dam was constructed.

"Allianoi was destroyed despite our efforts to save the baths. The government preferred profit over the preservation of such an important heritage site," said Ahmet Yaras, an archaeologist at Thrace University. Yaras, who spearheaded the efforts to save the archaeological site, has been refused a digging permit for the past three years. He added: "It feels like I'm being punished by the Turkish government because I tried to save Allianoi."

The eastern garrison town of Zeugma from 300BC is another historical site lost to the waters of a large dam project. Hasankeyf, a bronze-age town on the banks of the Tigris, is awaiting a similar fate.

In the central Anatolian town of Konya, the 5,000-year-old Askar Hoyuk burial ground was recently covered over with concrete and turned into a recreational area.

At Yenikapi, where a Byzantine harbour and 8,000-year-old human remains were found, the Turkish prime minister, Recep Tayyip Erdogan, recently outraged the archaeological community by ordering the excavation there to come to a rapid end as it was holding up construction of the prestigious Marmaray tunnel underneath the Bosphorus, which is aimed at easing traffic congestion in Istanbul.

A Turkish archaeologist, who did not want to be named, said he was heartbroken that the government appeared to be destroying sites at the same time as battling for the return of artefacts. "I don't understand the attitude of the government," he said. "This contradiction is truly mind-boggling.

"Of course, [the Turkish government] has the right to demand the return of certain artefacts, but they should never try to do this by threatening foreign excavation sites," he added. "One thing should not be confused with the other."

Asked if he felt Turkey had if not a moral claim then a legal one on the return of certain treasures, Parzinger said: "You have to understand that it was right at the time to bring these objects [to Germany] in order to protect them, but the times have since changed."

The Pergamon altar, which is one of the most popular tourist attractions in Berlin, was narrowly saved from destruction in the 1860s by the German engineer, architect and archaeologist Carl Humann.

"Many believe that the Pergamon altar stood in the Anatolian sun until the Germans dragged it away," said Parzinger. "But the truth is that Humann had watched in horror as reliefs were being loaded into lime kilns … on the basis of contracts made according to the law governing antiques at the time, it was arranged for the reliefs to be brought to Berlin and so it was saved." He said that while the Turkish authorities had discussed requesting the return of the altar, Berlin had never received an official request.