The "proposed transit priority route" would link the Joondalup city centre to the Wanneroo city centre, then south to Whitfords train station, Whitford activity centre, Hillarys Boat Harbour and Warwick train station.
Mayor Troy Pickard said it was disappointing to see a "lack of public transport aspiration for the northern corridor".
"It is out of touch with not only the aspirations of the community but out of touch with reality and a pathetic S-route through the City of Wanneroo and Joondalup is just that," he said.
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READ NOW"(The WA Planning Commission) needs to reflect the growing demands of the community for increased public transport in and out of Joondalup, which will be the State's first primary activity centre behind the Perth CBD."
Joondalup councillors at last week's meeting endorsed the City's submission on the draft documents, which addressed the need for a "bold vision and plan", increased employment self-sufficiency in the cities of Joondalup and Wanneroo, focus on growing the Joondalup city centre, tourism, improved transport connections and recommendations for a rapidly growing population.
"This report reflects the aspirations of Joondalup in 1980," Mr Pickard said. "Staff at the commission are asleep at the wheel if they think this document reflects the aspirations of the City of Joondalup and our community in 2015."
According to a council document, the City's assessments and forecasts show far higher commercial development and employment occurring in Joondalup.
It said the plan had proposed the Joondalup city centre have 20,181 jobs by 2050, an increase of about 3000 jobs from 2015, but since 2008, employment in the city centre had grown from 13,994 to more than 17,000, more than 400 jobs per year.
The City's forecasts estimate the city centre will accommodate 45,000 employees by 2050.
"I think we have a strong, well-documented case to demonstrate some of the figures in the report, particularly employment growth and economic development issues, don't stand scrutiny," Joondalup chief executive Garry Hunt said.
"It is not recognising Joondalup for what it is today, let alone what it is going to be.
"We've had 400 new jobs per annum in the city centre and for that to suddenly stop just does not make any sense."
Cr Brian Corr said the planning documents were "clearly leaning towards the development of Yanchep" with 23,000 jobs by 2050 estimated. Mr Pickard said Yanchep had always been designated a strategic metropolitan centre along with Joondalup.
"I think it's important to acknowledge that Joondalup is 30 years ahead of the development of Yanchep and in 30 years time, Joondalup will still be 30 years ahead of the development of Yanchep," he said.
He said the planning commission needed to recognise the "important hierarchical role" Joondalup has in the development of the metropolitan area and ensure the targets reflected that role.
The submission also indicated transport connections from the Joondalup activity centre to the Wanneroo city centre and Neerabup, Wangara and future east Wanneroo, the coast and future Ocean Reef marina, Burns Beach foreshore and Whitfords activity centre be made a priority and Joondalup Health Campus be designated a full tertiary hospital.