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

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 the Iranian regime to negotiate.

At a Downing Street press conference, he defended his decision to block initial offensive strikes by the US and Israel at the weekend, saying he “stands by” his judgment but denying that it had damaged the special relationship.

However, Starmer has faced some criticism from Gulf states and Cyprus for failing to do enough to protect regional allies and British citizens there from Iranian strikes. He has also been subject to personal attacks from Trump.

The prime minister insisted that “all ministers” on the national security council had supported the UK position on the use of British bases, after reports he faced cabinet opposition, led by the energy secretary, Ed Miliband.

In response, he told reporters that the UK would deploy “military and diplomatic strength” to protect British citizens, including four more Typhoon fighter jets being deployed to Cyprus on Thursday, as well as two anti-missile helicopters.

But in a firm reprimand to his critics at home and abroad, he added: “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.

“Now 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 on 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, was in Cyprus on Thursday.

Asked whether Trump – whom Starmer last spoke to on Saturday night – was right to suggest he had undermined bilateral relations, he said the special relationship was “in operation right now” at UK bases where forces were working with their American 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 now arrived back in UK on commercial flights from the UAE, with a further seven due to leave for UK on Thursday. The first government charter flight from Oman took off on Thursday with additional flights expected.

However, Starmer had a warning 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 he pushed to allow 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 … We then worked in through, the decision on Sunday, which was a decision of all ministers among us, that we should take the action that I then announced.”