Commonwealth backing was stripped for five road and rail projects, including a heavy haulage roadway and a freight network in the state's south amid an overhaul to rein in spending.
Mr Cook said the cuts would cause WA "pain" and the state was paying for "large unmanageable, unsustainable and unfunded projects on the east coast".
"We're part of the national spending program so we are impacted by the mismanagement or cost overruns in other states," he told reporters on Thursday.
"That's unfortunate, but it's part of being a national funding program."
He vowed to push on with the transport infrastructure projects, saying none would be cancelled or delayed.
"We will make them happen," he said.
"They are important economic enablers that are important for our local community."
Mr Cook called on the Albanese government to reconsider its decision to slash future financial contributions to new major infrastructure projects.
"We will definitely be impacted by the 50-50 decision," he said.
In a major funding overhaul earlier this week, the Commonwealth said it would contribute 50 per cent of major project funding going forward.
It previously fully funded projects or at an 80-20 split with the states.
He said WA was a "crucial economic enabler" and some of the defunded transport developments were links to major industrial projects that provide income for the nation.
"Over 30 per cent of the ... national highway network is in (WA) so we have a unique set of challenges associated with the maintenance and the development of that national Australian transport infrastructure," he said.
A freight network in the Great Southern region and a heavy haulage road south of Perth are among the projects the federal government has axed funding for.
The infrastructure review also put aside money for seven projects, with upgrades to a dusty outback road through the iron ore-rich Pilbara region and a congested traffic corridor through inner Perth.
The Commonwealth will also contribute a billion dollars to Perth's METRONET public transport project to build 72km of new passenger rail and 23 new train stations.
AXED WEST AUSTRALIAN INFRASTRUCTURE PROJECTS:
* Future road and rail connections for Perth
* Great Southern secondary freight network - $6.4 million
* Marble Bar Road upgrade - $48 million
* Moorine Rock to Mount Holland road upgrade - $48 million
* Pinjara heavy haulage deviation stages one and two - $200 million
