"There's plenty, clearly plenty, of unhappy people here, but she's made a very principled decision to say that politics isn't for her," Mr Shorten told reporters on Thursday.
"She's put her party and the people first. I actually now think that it's time for some of the personal attacks to stop. It's what turns people off politics."
Mr Shorten refused to say if he was happy with the NSW Labor investigation, which was widely leaked to the media.
"Emma Husar has been under extreme pressure, and I don't know all the facts at the end of the day," he said.
After announcing she would quit, Ms Husar accused some in the party of resenting her election because she had not come through the party machine.
"I had not done my Labor Party apprenticeship," she told the Nine Network.
"A few nasty, faceless people can ruin someone's career, almost completely smash it to pieces."
Prime Minister Malcolm Turnbull asked Special Minister of State Mathias Cormann about the bullying allegations, and he was told there were processes in place to help the former electorate office staff who complained.
That could include complaints to the Finance Department, and the Independent Parliamentary Expenses Authority.
"Those processes are managed by Finance or IPEA independently and confidentially in the appropriate way," a spokeswoman for Senator Cormann told AAP.
Mr Turnbull questioned how much Mr Shorten knew about the investigation.
"Where was the champion of the workers when people were being allegedly mistreated in this way?" he told 6PR radio in Perth.
But the Labor leader insisted he only found out when the story was leaked to the media.
"It's rubbish. I had no knowledge of these complaints," Mr Shorten said.
Ms Husar's western Sydney seat of Lindsay, held with a margin of just 1.1 per cent, will be hotly contested between Labor and the Liberals at the election due by May 2019.