Greece has become the latest European country to raise pressure on aid groups that help asylum seekers, accusing them of involvement in trafficking, as part of its efforts to stem the flow of migrants and refugees who continue to make dangerous journeys to Europe.

The country has launched criminal investigations into several organizations in the past year, while also imposing new requirements on registering with the government.

Aid groups say it is part of a wider pattern of Greek authorities trying to discredit them and make it harder for them to operate, under the assumption that fewer migrants will come to Greece if there are fewer nongovernmental organizations helping them when they arrive.

“We have seen over the last two years an intensification of the crackdown and criminalization of NGOs working with migrants and asylum seekers,” said Eva Cossé, a researcher with Human Rights Watch. “The point is to intimidate and harass them. It has already created a chilling effect in civil society.”

Greece’s government says its measures are aimed at stopping human trafficking. “We don’t want to be the gateway to Europe for illegal migration or smuggling networks. Also we have done a great job of countering smuggling networks, dismantling them,” said Alexandros Ragkavas, spokesman for the Greek Ministry of Migration and Asylum.

Greek authorities have used a variety of tactics in recent years to reduce the number of people who cross the Aegean Sea or Greece’s land border with Turkey, and either claim asylum or continue on to other European countries such as Germany.

Karatepe refugee camp, on the eastern Aegean island of Lesbos, Greece.

Photo: Panagiotis Balaskas/Associated Press

Testimony from numerous migrants suggests Greek authorities last year began escalating their use of pushbacks, or forcible extrajudicial deportations of migrants who have just entered Greece by sea or land, as well as rounding up migrants from inside Greek territory and sending them back across the Turkish border.

Greece has repeatedly denied using pushback tactics, dismissing all evidence and reports in international media as propaganda by its geopolitical rival Turkey. Despite Greece’s denials, European Union authorities have criticized the practice of pushing back migrant boats, with EU Commissioner for Home Affairs Ylva Johansson telling the government in July to stop such actions, which she called “violations of our fundamental European values.”

Now, Greek authorities are increasingly going after the aid groups that assist asylum seekers or that document the pushback tactics.

Greece, like Italy and Malta before it, say that such aid groups as well as rescue boats encourage migrants to undertake dangerous sea crossings to Europe in the expectation that they will be assisted.

On July 19, Greek prosecutors announced a criminal investigation into 10 people, including four NGO workers, “for the offenses of facilitating the illegal entry of foreigners into Greek territory, espionage, complicating investigations by the Greek authorities, as well as other violations of the immigration code.” They were also accused of “providing substantial assistance to organized circuits of illegal trafficking of migrants.”

Police didn’t name any individuals or organizations, but Tommy Olsen, founder and head of Aegean Boat Report, learned from leaks to Greek media that they were being investigated.

Greek police didn’t respond to repeated requests for comment about the investigations.

Mr. Olsen’s group publishes reports on Greece’s pushbacks and advises migrants and refugees once they have arrived ashore on how to prove they were in Greece, where the authorities are supposed to process any asylum claim they make, in case they are later pushed back.

Migrants send him photos and videos of distinctive landmarks on Greek islands such as churches and road signs, which can constitute evidence in case their legal rights are later violated.

“If the Greeks go through their phones and see that migrants shared information with me, they use this as evidence of human trafficking or that I’m trying to disrupt police work on the ground,” Mr. Olsen said.

Syrian NGO Josoor learned from leaks to Greek media in late 2020 that it was under investigation, said Natalie Gruber, co-founder and spokeswoman for the group.

The group says it still hasn’t been contacted by Greek police or prosecutors. Nevertheless, being reportedly under investigation has cost it funding and staff. Team members have left for fear of ending up on trial and donors have rescinded about 40,000 euros, equivalent to $47,000, in pledged funding, Ms. Gruber said.

“I see this as just another part of the European border regime’s deterrence policy,” she said.

Last year, Greece’s migration ministry began introducing stricter legal and regulatory criteria for NGOs and requiring them to submit to a lengthy registration process. About 65 aid groups working with migrants have been rejected under this process, although they are allowed to reapply, said Mr. Ragkavas, the ministry spokesman.

Greece also recently designated Turkey as a safe country for five major nationalities of migrants—Somali, Bangladeshi, Afghan, Pakistani and Syrian—meaning that they should seek asylum there and making it unlikely that they can qualify for asylum in Greece.

Despite the recent criticism of pushbacks from the European Commission, most EU officials and other European governments have been broadly supportive of Greece’s efforts to stop migrants arriving in the continent.

Ms. Cossé, the Human Rights Watch researcher, said it is too early to tell whether European authorities will put pressure on Greece to rein in its tactics against migrants and NGOs.

In her meetings with EU officials in Brussels she senses “that there has started to be some fatigue” about Greece’s actions, especially the pushbacks, she said.

“They are happy that Greece is doing the dirty work,” she said of the EU, “but at the same time there is a limit.”

Write to Raja Abdulrahim at raja.abdulrahim@wsj.com