The deal between Sunak’s government and Kigali is set to witness asylum seekers who reach England's southern coast in small boats sent to the East African nation.
However, in June 2022, the ECHR issued a last-minute injunction - known as interim measures under Rule 39 - to prevent the first deportations. Last November, the UK Supreme Court also ruled that the policy was unlawful because of failings in the Rwandan system.
To overcome this, a bill is going through the British parliament to declare Rwanda safe and give ministers power to decide whether to enforce ECHR injunctions.
"There is a clear legal obligation under the convention for states to comply with Rule 39 measures," ECHR president Siofra O’Leary told reporters in Strasbourg.
Where states had failed to comply with injunctions, issued "in exceptional circumstances where there is a real and imminent risk of irreparable harm," the court had ruled they had violated the European Convention on Human Rights, O'Leary said.
O'Leary pointed out that Britain itself had publicly urged other states to comply with Rule 39 orders, the most recent being for Russia to release Kremlin critic Alexei Navalny in 2021.
In response, Sunak's spokesperson said the government was confident the bill complied with international law.
"There should be no need for Strasbourg to intervene to block flights in the way that they did in 2022," the spokesperson said, adding, "the prime minister has been clear repeatedly that we will not let a foreign court block flights from taking off."
The Rwanda policy is one of Sunak's key pledges ahead of an election expected this year.
The prime minister is under pressure both from right-wing lawmakers in his Conservative Party and from voters concerned about thousands of asylum seekers arriving without permission across the Channel.
Almost 30,000 people made the journey last year and Britain spends more than 3 billion pounds ($3.82 billion) a year processing asylum applications.
Britain also pays 8 million pounds a day for housing for those awaiting a decision.
Last week, lawmakers in parliament's lower House of Commons backed Sunak's "Safety of Rwanda Bill" despite a rebellion by his right-wing critics who said the bill was not tough enough to ensure judges could not block deportations.
However, O'Leary's remarks might provide succor to critics. On Monday, lawmakers in parliament's upper house backed a symbolic motion to delay ratification of a new treaty with Rwanda and they could seek to amend the bill when it comes before them next week.
The role of the ECHR is to apply the European Convention on Human Rights on the 46 members of the Council of Europe, issuing binding judgments on those states should they commit violations. While Britain has left the European Union, it remains a member of the Council of Europe.
Forum