Senate crossbenchers have gutted government legislation to overhaul workplace relations laws that limit union bargaining timeframes for large construction projects.

In order to get a least some measures through the upper house, the federal government struck a deal with the crossbench to support amendments to drop six of the nine major changes to the Fair Work Act.

What remained when the bill passed through the Senate  was a requirement that bosses discuss an application for unpaid parental leave with employees before dismissing it.

The amended bill also prevents protected-action ballot orders – which authorise industrial action – being issued before bargaining with the employer starts.

The most substantial win for the government was changes to greenfields agreements – which are struck between employees and unions on large-scale construction and resources projects.

The government wants to stop unions exploiting their role in the agreement to seek excessive wage claims and hold up projects, which imposes significant costs on organisations.

The changes allow an employer to take an agreement to the Fair Work Commission for approval if a deal hasn’t been struck within a certain timeframe.

However, even that change was amended by the crossbenchers to extend the timeframe from three to six months and to impose two-yearly reviews of the rules.

They also scrapped plans to restrict when union officials can visit a worksite, alter individual flexibility agreements and scrap worker allowances in unpaid annual leave.

The changes would have required a worker to request the attendance of a union official for them to be allowed on site.

Labor has been staunchly opposed to the measures, which it believes is an attack on workers.

Opposition senator Anne McEwen said the bill was an example of the coalition seizing every opportunity it could to return to its “ideological nirvana of work choices”.

Labor frontbencher Doug Cameron accused the government of wanting to stop collective bargaining altogether.

But government senators launched into stories of bullying by union officials to justify the measures.

Liberal backbencher David Johnston said the Fair Work Commission should be able to deal with excessive visits to worksites.

He said uninvited “lunchroom invasions” on workers enjoying their meal in peace were a “bizarre, bizarre blank cheque” handed by Labor to militant union groups like the CFMEU.

The government remains committed to pushing all the measures through the parliament, having promised the overhaul prior to its election.

The bill now goes back to the House of Representatives for final sign-off.