An account of the meeting to AAP stated there had been anger between executive members and deep resentment within sections of the party boiled over during discussion of the recommendation in Perth on Saturday.
WA Liberal Party state president Norman Moore rejected that account.
The WA Liberal policy calls for more defence assets to be located in the state in preparation of a possible heightened Chinese presence in the Indian Ocean.
Its terms of reference were broadened to remove the focus on China after Ms Bishop's office intervened due to concerns it would anger Beijing.
Ms Bishop defended her office's recommendation during her address to the council, drawing hostility from at least one executive member who questioned her authority to intervene, AAP understands.
An amended version of the original motion, citing "heightened foreign naval activity," will now be put forward for debate at a Federal Council meeting in Sydney later this month.
A spokesperson for Ms Bishop denied the meeting was tense.
"That is an inaccurate account of what was supposed to be a confidential discussion," they said in an email.
When retired WA Liberal senator Alan Eggleston proposed for an increased military presence on the state's north coast last month, he stated concerns over the security of shipping lanes passing through the Indian Ocean, in close proximity to oil and gas resources.
"Informed US-based investors in the oil and gas industry feel that Australia has an obligation to provide more locally based military protection given the increase in terrorist events around the world including in the countries to our north," the document says.
"West Australian LNG, iron and salt from the Pilbara use the Northern Indian Ocean trade routes are vulnerable.
"Concern has been expressed that Pakistan is likely to permit Chinese naval vessels to use their Indian Ocean-based ports as bases for the Chinese Navy which would dramatically change the strategic balance in the north west Indian Ocean which could have serious implication for Australian trade and supply of oil."
A Royal Australian Navy base is located south of Perth, while there are three RAAF bases across Western Australia, in Exmouth, Derby and north of Perth.
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