Asked whether he felt for the cleaner, Mr Henare told reporters: "Here's the question - if she doesn't want the job, give it to somebody else that wants the job."
He added: "I'm not the employer. Are we supposed to feel sorry for every person in New Zealand who's got a hard job?"
Labour Party spokesman for Labour issues Andrew Little said Mr Henare's comments reflected the attitude of many employers.
"It is a culture in a lot of workplaces now - 'If you don't like it, just leave and go somewhere else'. That's not an answer. If you're being treated unfairly, you take it up with your employer and you push back."
He said Mr Henare's comments were "sad" because the National MP was a former union official.
Mr Henare said on Twitter last night that he had previously cleaned toilets himself.
He added: "I apologise to the lady and to all those that haven't really got a choice in jobs. Aroha mai. My bad."
Ms Sinoti was one of three cleaners who made a joint submission on sweeping changes to the Employment Relations Act.
She told the committee: "You never see us. Every evening we say goodbye to our family, and catch the bus or train from Porirua or Wainuiomata to clean your office.
"We vacuum the floors, scrub the toilets and tidy away your rubbish. We come in at midnight when you have all gone home, and the Parliament's buildings are empty.
"It is impossible to manage on a cleaner's wage. It cost me about $100 or more to travel to work."
The cleaners were especially concerned about the scrapping of a rule which required companies with fewer than 20 employees to keep workers on when a contract changed.
Ms Sinoti said: "We are what they call vulnerable workers, because our employers are contractors who constantly win and lose contracts.
"Now we face uncertainty again, because if this change happens, contractors can do whatever they like and sack us cleaners when they have [won] the contract of our employer."