Mr Nalder told a business breakfast last week that being able to deliver a twin-bored tunnel railway line out to Forrestfield as part of the $2 billion airport link at a price in line with doing it above ground meant he "felt a lot more comfortable to explore this as a potential solution for getting us to the port".
The other option is to continue the freight link down Stock Road and Leach Highway/High Street.
Mr Nalder said part two was yet to be finalised, but he did apologise to Palmyra residents for the uncertainty created while he explored alternative routes.
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READ NOWA Palmyra resident said her family was working around the clock to finish renovations so they could be compensated appropriately if the State Government resumed her home.
"We�ve just been spending money to try to get it finished potentially so they can knock it over," she said.
Fremantle MLA Simone McGurk argued the uncertainty was widespread and the project should be scrapped.
A City of Melville report by technical services director John Christie in July found 72 commercial and residential properties would be affected if the Stock Road/Leach Highway option went ahead, "from full acquisition to minor land take to changes in access".
Of the 46 residential properties, 20 are in Palmyra, 21 in Willagee and five are in Hamilton Hill and Fremantle.
"The City is firmly of the view that Option 2 with a tunnel under the Fremantle Eastern Bypass alignment is the best outcome for the community, the long-term operation of the Perth Freight Link and Fremantle Port," Mr Christie said.
Cockburn Mayor Logan Howlett said he welcomed news the Senate would investigate the financing and decision-making behind the freight link in September or October.
Mr Howlett was hopeful information that parties opposed to the $1.6 billion project have been looking to scrutinise for months would be made public.
"Transparency is of the highest priority, particularly when you're spending billions of dollars of taxpayers" money on a project which the community are generally saying they don't want and there's better options available,� he said.