Ziad Basyouny will run against Tony Burke in Watson and Ahmed Ouf against Jason Clare in Blaxland, with Labor holding both seats on 15 per cent margins.
Backed by political groups The Muslim Vote and Muslim Votes Matter, the two candidates had spoken to all rival candidates and parties about preference flows and planned on putting Labor last.
But the Liberals have ruled out a deal.
"The Liberal Party will place the three declared 'Muslim Vote' candidates running in Blaxland, Calwell and Watson below the Labor Party on our how-to-vote materials," a spokesperson said.
About one-third of Blaxland and about one-quarter of Watson and Calwell are Muslim.
Calwell in Melbourne's north is held by retiring Labor MP Maria Vamvakinou on 12.4 per cent, although independent Samim Moslih has received less attention.
While political pundits wouldn't usually watch the safe seats on election night with the Liberals running dead in Blaxland and Watson, the high-profile independents sparked a conversation about whether community backlash over Gaza could turn the dial.
Muslim Votes Matter is targeting seats with high proportions of Muslims in Melbourne, Sydney and Western Australia and aims to pressure Labor into taking more action in support of Palestine.
But the Muslim and Arab communities of Sydney's west are far from homogenous, with Mr Clare a largely popular local member who has received the backing of Auburn's Gallipoli Mosque.
Mr Clare has been stronger in his condemnation of Israel on the war in Gaza, including for bombing schools and hospitals, and has consistently called for a ceasefire.
"Peter Dutton said it was a mistake to let people from Lebanon migrate to Australia, Peter Dutton said it was wrong to let people fleeing Gaza come to Australia, so to say that two parties are the same is just wrong," he told AAP.
Without the Liberal preferences it would be very hard to dethrone Labor, election analyst Kevin Bonham said.
Labor's primary vote would need to be knocked down to the low 40s or high 30s for the independents to have a chance and then Liberal preferences would be needed to get them over the line if they poll second, Dr Bonham said.
Mr Clare scored a 55 per cent primary in 2022 while Mr Burke collected 52 per cent of first preference votes.
Labor took an almost 10 per cent swing against its primary vote in Calwell in 2022, dropping down to 45 per cent.
But the seat is a more traditional Liberal-Labor contest with the Liberals gaining more than seven per cent of the two-party vote at the last election.
Dr Basyouny and Mr Ouf say the government's failure to adequately condemn Israel for collective punishment and killing tens of thousands of people in Gaza spurred them to run, as it highlighted injustice in the community.
The Liberals preferencing independents highly critical of Israel and pushing for more action on Gaza would open it up to attacks following their strong rhetoric supporting Israel, Dr Bonham said.
"Some Muslim community-type independents are going to appeal to voters partly by being seen as being pro-Gaza and that makes it dangerous for the coalition to allocate preferences to them," he told AAP.
A similar point was made by a senior Labor source who said any preference deals by either of the candidates with the Liberals would spark outrage in the community, given Mr Dutton's stance on Gaza.
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