Keir Starmer has said the conflict engulfing the Middle East could continue “for some time” as he insisted the best way forward in the longer term was a negotiated settlement with Iran.

The prime minister said the UK was doing “everything we can” to de-escalate the situation, a clear contrast to the US president, who is focused on regime change and has said it was “too late” for Tehran to negotiate.

He defended his decision to block initial offensive strikes by the US and Israel at the weekend, saying he stood by his judgment and denying it had damaged the special relationship.

Starmer has faced some criticism from Gulf states and Cyprus for not doing enough to protect regional allies and British citizens there from Iranian strikes. He has also been subject to personal attacks from Trump, including that he was “not Winston Churchill”.

But the prime minister has urged the US president to de-escalate the conflict and negotiate with Iran to abandon its nuclear programme. Trump, meanwhile, has said he needs to be personally involved in selecting Iran’s next leader.

Starmer insisted that “all ministers” on the national security council had supported the UK position on the use of British bases, rejecting reports he had faced cabinet opposition led by the energy secretary, Ed Miliband. The Guardian understands, however, that all options were discussed at the NSC meeting on Friday.

In response to claims his response had been characterised by “indecision, prevarication and under-preparation”, the prime minister told reporters the UK would use “military and diplomatic strength” to protect British citizens, and would deploy four more Typhoon fighter jets and two anti-missile helicopters to Cyprus on Thursday.

But in a firm reprimand to his critics at home and abroad, the prime minister said: “It means having the strength to stand firm by our values and our principles, no matter the pressure to do otherwise.

“The longstanding British position is that the best way forward for the regime and the world is a negotiated settlement with Iran where they give up their nuclear ambition.

“That’s why I took the decision that the UK would not join the initial strikes on Iran by the US and Israel. That decision was deliberate. It was in the national interest, and I stand by it.”

Starmer, who attended his second Cobra meeting about the conflict on Thursday, insisted the UK would “maintain the shield” over British people in the region, as well as allies.

The defence secretary, John Healey, who was in Cyprus on Thursday to calm the diplomatic fallout over a drone that evaded detection and hit RAF Akrotiri, accused opposition politicians of deliberately undermining the UK’s relationship with Donald Trump. He said it was unpatriotic for MPs to seek to turn the US against Starmer.

The prime minister rejected Trump’s claims that he had damaged bilateral relations, saying the special relationship was “in operation right now” at UK bases where forces were working with their US counterparts.

“That is the special relationship. That is a special relationship in operation, and clearly, it’s for the president to take decisions that he considers in the national interest the right decisions for the US,” he said.

“I understand that, I respect that, but equally, it’s for me as the British prime minister to take decisions that I consider to be in the best interest of the UK. There’s nothing controversial about that. The special relationship is operating right here at an important point.”

More than 4,000 people have arrived back in UK on commercial flights from the UAE, and a further seven such flights were expected to take off on Thursday. The first government charter flight from Oman took off on Thursday and more flights expected.

Starmer sounded a note of caution, however, for hundreds of thousands of Britons still stuck in the region. “This is a huge undertaking. It is one of the biggest operations of its kind … Many times bigger than the evacuation from Afghanistan. It is not going to happen overnight. But we will not stop until our people are safe,” he said.

Starmer did not deny that he had raised the question of allowing the US to carry out defensive strikes from British bases but faced opposition from some of his cabinet on Friday. Instead, he said there was no formal request from the US until Saturday.

“Let me be really clear about this: no request from the US came in the specific terms that we acceded until Saturday afternoon. Therefore on Friday, there was no concrete decision to be made,” he said.

“We then, as you would have expected, went through the details with the US over the next day … The decision on Sunday was a decision of all ministers among us, that we should take the action that I then announced.”

The British public appears to back his position for now. YouGov polling shows that 46% think the UK military stance should be purely defensive, tasked with shooting down drones and defending civilian areas and UK military facilities.

A quarter (26%) say the UK position should be retaliatory only, targeting missile sites that have launched attacks against civilians and British military bases, but otherwise not getting involved. Only 8% of Britons think the UK should actively join the US and Israeli-led attacks on Iran.