The findings, by the National Infrastructure Commission (NIC), also called for improvements on the most congested part of the M62 to be sped up.
The body, set up by the government to advise it on economy boosting-projects, said the region needed "immediate and very significant investment".
At present, ministers are due to commit £300 million for transport projects later this week, reports BBC News.
More information on future schemes is expected to be announced during the chancellor’s Budget speech on Wednesday – despite almost half of the money touted for transport being announced in last year’s Autumn Statement.
George Osborne will also commit £75 million of the pot to explore plans for a new trans-Pennine road tunnel and bring forward £161 million for upgrades to the M62 Liverpool-Hull motorway.
Speaking on BBC Radio 4’s Today programme, chair of the NIC and former Labour transport secretary Lord Adonis said transport improvements in the north were already being started.
He said the planned work, including the electrification of the railway line between Manchester and Leeds, should be "seen as the first stage on the road" towards HS3.
Lord Adonis believed the electrification of the line would slash journey times to 40 minutes and, once HS3 had been completed, down to 30 minutes between the two cities.
A full blueprint for HS3 will be drawn up next year.
"This is going to be a phased approach. It’s not going to be one big bang like HS2, which is the creation of a completely new line for nothing," Adonis told the BBC.
"It will be a mixture of improving the current line and stretches of new line to deliver two objectives: big cuts in journey times between the big northern cities, from Liverpool in the west to Hull in the east, and also big improvements in capacity, so you can have much more regular trains as well as faster trains," he added.