The inquiry will seek to explain how passports bearing the names of six British-Israelis, who are not the men pictured, came to be used.
Israel's secret service, Mossad, has been accused of involvement in the killing in Dubai on 20 January.
Mr Miliband refused to reveal what was said in the 20-minute meeting between Israeli Ambassador Ron Prosor and Sir Peter Ricketts, the head of the UK's diplomatic service.
Speaking on the Jeremy Vine show on BBC Radio 2, he said: "It's very, very important that we don't make accusations until we know that they're well founded."
He added: "Any interference with British passports is an outrage. We take this case extremely seriously - the integrity of our system is critical."
Mr Prosor told journalists after his meeting that it is "not the usual way to talk about what happens in those meetings".
In Dublin, Israeli ambassador Zion Evrony also insisted he knew nothing about the killing of the Hamas commander.
The Ambassador said that he had no information on the matter and would relay the messages he had received to his authorities.
British Conservative leader David Cameron called for Israel's ambassador to the UK to be asked "some pretty tough questions".
Meanwhile, shadow foreign secretary William Hague has urged the Foreign Office to confirm when it first knew about the fake passport claims.
UK diplomats said they had received details of the British passports a few hours before Dubai released details on Monday.
Israeli ambassador Ron Prosor on the Dubai murder
However, Mr Hague told BBC Radio 4's Today programme it was "entirely possible" the government had been alerted to their use in January.
He later said Israel should issue a "robust statement" ensuring its government would not sanction the cloning of British passports.
Lib Dem foreign affairs spokesman Sir Menzies Campbell said any abuse of British passports was an infringement of British sovereignty and the Israeli government should act to end a "raft" of speculation.
The BBC's Middle East editor Jeremy Bowen said if there was proof Israel had used British passports "for some nefarious uses of its Mossad service - as they have in the past with Canadian and New Zealand ones", then relations between the UK and Israel would be "in a crisis".
The Serious Organised Crime Agency has confirmed photographs and signatures on the passports used in Dubai do not match those on passports issued by the UK.
The men whose names appeared on the passports have dual British and Israeli citizenship.
They are Melvyn Adam Mildiner, Paul John Keeley, James Leonard Clarke, Stephen Daniel Hodes, Michael Lawrence Barney and Jonathan Lewis Graham. They all deny involvement in the killing.
Hamas killing
Police in Dubai have released images of 27 people they believe are behind the killing of a senior Hamas commander. The suspects are accused of using fake passports bearing their own pictures, but the names of innocent citizens.
Twelve of the passports used were British (shown on previous slide). The other 15 on the list are reported to have used stolen identities from Australian, French, Irish and German citizens.
The 27th suspect used the alias Joshua Aaron Krycer - a stolen Australian identity (pictured left). Police say the suspects used their fake documents to travel to Dubai in groups, flying from Zurich, Rome, Paris and Frankfurt.
One of the victims of the identity theft was British-Israeli Paul John Keeley (pictured right). The passport used by one of the suspected assassins bore his name, but featured a photograph of another man (pictured left).
Palestinian militant Mahmoud al-Mabhouh was killed in his hotel room in Dubai on 20 January. Police claim one of the suspects, pictured on the left, went to a hotel to put on a disguise. He is seen leaving a toilet wearing a wig.
Surveillance cameras also recorded Mr Mabhouh, circled in red above, at the hotel's reception before his death. At the bottom of the image the head of one of the suspects can be seen. As Mr Mabhouh leaves, the suspect follows.
Mr Mabhouh is trailed into the lift by a number of the suspects, including two pictured here in tennis gear. Investigators believe he had been followed from Syria to Dubai where it is thought he wanted to buy weapons for Hamas.
When Mr Mabhouh leaves the lift, police say two of the suspects can be seen following him down the corridor. He was later found dead in his room. A post-mortem report said he had been electrocuted and suffocated.
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The details of the suspects and their passport photos were released by officials in Dubai earlier this week.
The Irish government has said passports used by three people believed to have been involved in killing a Hamas member had genuine numbers.
However, authorities said while the numbers were legitimate, they did not match records for the names which had been used - Gail Folliard, Evan Dennings and Kevin Daveron.
Dublin's Department of Foreign Affairs said officials were urgently trying to contact the three citizens who hold or have held passports with these numbers.
In a statement it said it took "grave exception" to the forgery, which could potentially put at risk the safety of Irish citizens travelling abroad.
France - and reportedly Germany - have raised doubts over the identities of two suspects who used a French and a German passport.
France's foreign ministry spokesman Bernard Valero said it was "demanding explanations" from the Israeli embassy in France about the circumstances of the use of a false French passport in the Dubai killing.
Reports have suggested the Hamas commander was in Dubai to buy weapons for the Palestinian Islamist movement, Hamas.
Two Palestinian suspects were being questioned about the murder. Police said the pair had fled to Jordan after the killing, but were extradited back to Dubai on Sunday.
Officials in Dubai, who have issued arrest warrants, said the team appeared to be a professional hit squad, probably sponsored by a foreign power.
"It is 99%, if not 100%, sure that Mossad is standing behind the murder," Dubai police chief General Dahi Khalfan is quoted as saying by an Abu Dhabi-based English-language paper.
The Respect MP George Galloway said assurances from Israel could not be trusted as the "rogue state" had broken its word in the past.
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CCTV of Hamas murder suspects released by Dubai police
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