Britain has embarked on a renewed war in the Middle East, starting with air strikes in the next 48 hours, after MPs overwhelmingly sanctioned a UK air assault against Islamic State targets in Iraq.

Cabinet ministers also told the Commons that Isis will ultimately only be crushed if the terrorist group is pursued to its bases inside Syria, signalling an eventual widening of the conflict that is expected to last several years.

Downing Street said six Tornado jets would be in the skies over Iraq very shortly, adding the Commons has sanctioned the sending of UK military advisers to Iraq to train the country's army and act as target setters for the RAF.

MPs voted by 524 to 43 to sanction the UK air strikes, limited to Iraq, with 69 MPs not voting. A total of 23 Labour MPs, five Tories and two Lib Dem MPs voted against UK action along with the SNP MPs and the Green MP Caroline Lucas.

The shadow education minister and MP for Tower Hamlets Rushanara Ali resigned before the vote in order to abstain, saying she feared "further air strikes will only create further bloodshed and pain in Iraq". She voted in both division lobbies to make what she called a "principled abstention" on the issue.

The scale of David Cameron's victory was predictable as soon as he reached an agreement with the Labour leader Ed Miliband establishing that a separate request would be put to MPs to sanction any action in Syria. The overall tone of the seven-hour debate was questioning, wary, and dubious. MPs on both sides repeatedly warned any strategy that did not address Isis in Syria, or the proxy power struggle war between Iran and the Shia on the one hand and the Saudis and the Sunni on the other was incomplete.

There were also questions over whether Iraq's army has the political will to defend Shia communities from Isis assault.

After the vote the defence secretary, Michael Fallon, said "You will not see an immediate series of particular hits. This is going to be a long campaign of weeks and probably months to drive IS. We will be very careful to avoid civilian casualties. Each of these missions will have to be personally authorised by me and there are clear rules of engagement."

There are already early signs that Isis has switched tactics to minimise its exposure by reducing roadblocks, the use of pick-up trucks and by placing Isis black flags in civilian areas. A sometimes nervous-looking David Cameron opened the debate by telling MPs "the hallmarks of this campaign will be patience and persistence, not shock and awe". He said there was "no option to walk on by", stressing there was a clear legal case to support the request of the Baghdad government to bring in its assets.

The prime minister argued that the threat from Isis was real: "This is not a threat on the far side of the world. Left unchecked, we will face a terrorist caliphate on the shores of the Mediterranean and bordering a Nato member, with a declared and proven determination to attack our country and our people.

"This is not the stuff of fantasy; it is happening in front of us; and we need to face up to it".

He added "this mission will take not just months, but years, and I believe we have to be prepared for that commitment "He added Sunni Arab states had to realise they had been mistaken in financing extremists groups in Syria.

Significantly, Cameron reserved the right to take military action beyond Iraq in the case of a humanitarian emergency or urgent national interests without prior consultation of parliament. But Downing Street explained it was taking a cautious step by step approach and would always seek the political authority of parliament.

Formally the resolution before parliament made it clear that a second vote would be obtained to authorise any ongoing non-emergency action in Syria.

The UK intervention in Iraq has come after a request for support from the Iraqi government, while the Syrian regime under President Bashar al-Assad is unlikely ever to do the same.

However, Cameron argued that this would not be a bar to military engagement in that country. Referring to action in Syria, Cameron said: "I don't believe there is a legal barrier, because I think the legal advice is clear that – were we to act or others to act – there is a legal basis".

Miliband argued that any action in Syria should be preceded by an attempt to secure a UN security council resolution, but the shadow foreign secretary Douglas Alexander said such a resolution was not indispensable to future Labour support, a position that would have handed a veto to Russia, a permanent member of the UN Security Council. Alexander said "our moral compass is not set in Moscow or Beijing".

Miliband, an opponent of the 2003 Iraq war, strongly defended the proposed air strikes saying "this is not a clash or civilisations", but a specific war to end the spread of Isis supported by the democratic government in Baghdad. Labour said President Assad had to be removed in Syria, but the lack of democratic military forces made UK involvement in Syria more complex.

Cameron himself disappointed many of his backbenchers when he said he was not going to arm the Free Syrian Army, something the US is already doing alongside its campaign of air strikes.

Barack Obama is planning to train as many as 5,000 Syrian fighters to combat both Assad and Islamic State.

But Fallon gave the impression that once UK politics permitted, the war would have to extend to Syria saying: "There is a strong case for action against Isil in Syria. Isil is based in Syria.

That's where its headquarters are, that's where its resources, its people are. They have crossed the border into Iraq and to deal with Isil, you do have to deal and defeat them in both Iraq and in Syria".

The former cabinet minister, Kenneth Clarke, said: "I still think that we are at the early stages of working out exactly where we are going. there is absolutely no doubt that ISIS has to be defeated in both countries".

The former defence secretary Liam Fox, a Conservative MP, said it had been a mistake to exclude Syria from air strikes saying "Isil operates from Syria. It attacks individuals, communities and the Iraqi state itself from Syria. There is a clear legal case for attacking Isil bases in Syria."

The Labour MP John McDonnell said: "This is madness and an absolute disaster. We are already talking about a mission creeps and a strategy that could last 3 or even 10 years … the war on terrorism will be brought to our streets as a result."