That works out to $289 a day for a backbench MP, $525 a day for Crown Ministers and the leader of the Opposition and $838 a day for the Prime Minister.
While the Prime Minister, other ministers and MPs are frequently away from Parliament on sitting days, they generally have a leave of absence. New rules setting out the criteria under which MPs are deemed to be absent without leave will be formulated by parties in consultation with the Speaker.
The committee has also recommended a new clause that imposes the same daily financial penalty when an MP is suspended or "named" by the Speaker for bad behaviour.
Suspension is a relatively rare sanction but has been used against New Zealand First Leader Winston Peters in recent years.
Constitutional law expert Graeme Edgeler said it had been a widely held myth that financial penalties already applied in cases of suspension.
Meanwhile, the committee's recommendation to ditch the bill's provision to move decisions about MPs' travel costs from the Speaker to the independent Remuneration Authority is in line with advice from the Clerk of Parliament Mary Harris.
Mary Harris suggested it contravened the principle of Parliament's privilege to control its operations.
She said getting MPs to Wellington was fundamental to them carrying out their roles in Parliament rather than a form of remuneration.
The committee rejected the same argument made in relation to accommodation expenses which will be set by the authority when the bill is passed.
"That's just where they live when they're in Wellington so it seems sensible that someone outside Parliament is working out what should happen there," Mr Edgeler said.
The committee says the authority should also make decisions about travel expenses for MPs' families.
Other recommendations made by the committee include a new provision to prevent double dipping when an MP is voted out at an election but returns to Parliament on the party list within three months - a period during which they continue to receive their salary.
In response to last year's furore over translation services for deaf Green MP Mojo Mathers, the committee also wants MPs' entitlements to services to take into account any physical or sensory impairments.
Pay up
Daily fines for MPs after three days unjustified absence:
• Backbench MP - $289
• Minister - $525
• Prime Minister - $838