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He told the BBC union officials were experienced in negotiating workplace harassment and bullying clauses.
The Independent Parliamentary Standards Authority offers guidance on grievance procedures as part of MPs' standard contracts but these are not binding.
Staff working in Parliament lacked a "collective voice", Mr Watson added.
He told BBC Radio 4's Today that sexism was an issue for all political parties and that Labour had strengthened its own procedures this summer before the current allegations of misconduct by MPs arose.
On Monday, ministers said the way the Commons handles complaints about MPs must be improved, with more specialist staff working on the confidential helpline and a contractually binding grievance procedure for MPs, peers, those working directly for parliamentarians and interns.
Mr Watson suggested the way that MPs agreed contracts with their staff needed to be reviewed to give the often "very powerless" people they employed more protection.
"IPSA basically tell MPs what contracts they can give their staff now and yet they don't represent trade unions," he said. "Trade union officials are specially trained to deal with allegations of harassment and bullying.
"They are trained negotiators so they can try and get harassment and bullying clauses in parliamentary contracts. It is not going to sort all these issues out but I think it is one way."
Mr Watson said Jeremy Corbyn had taken a strong stand on the issue of abuse within Labour. Sheffield Hallam MP Jared O'Mara was suspended recently pending an investigation into a number of misogynistic remarks, for which he has apologised, and alleged homophobic comments.
"I don't think harassment, bullying and abuse rests with one party," Mr Watson added. "It is across the whole of society. We need to deal with our own issues."
The party's national executive committee had approved a new set of procedures in July, he said, including a new confidential helpline for reporting alleged misconduct and more compliance officers.
In the wake of recent allegations about MPs' behaviour, the Unite union said there needed to be a bullying and harassment policy covering everyone working in the Palace of Westminster.
"Political parties can't be left to deal with these issues themselves as it will only lead to inconsistencies in how people's complaints and concerns are dealt with," a spokesman said.
The union, which says it provides support and advice to hundreds of people working in Parliament, also called on the independent watchdog to do more and "reconsider its repeated failure to recognise Unite's parliamentary branch for employment and collective bargaining purposes".
IPSA has said it had expressed concerns about HR support for MPs' staff but following a consultation last year with MPs and the Commons authorities it was decided its role should not be widened to cover such issues.
On Monday evening, a spokesman for Defence Secretary Sir Michael Fallon said he apologised in 2002 after being rebuked by a journalist for putting his hand on her knee during dinner.
Radio presenter Julia Hartley-Brewer had recounted the "mildly amusing" incident without naming Sir Michael.
After his identity was revealed in The Sun, she tweeted saying she had not been "remotely upset or distressed".
Ms Hartley-Brewer, a former political editor of the Sunday Express and regular political commentator, has criticised "wild rumours and claims" circulating at Westminster. She said she did not consider herself a victim after the incident which happened over dinner at the Conservative Party conference.