Zimbabwe's government says sanitary towels donated during an international appeal must be quality tested before any duty exemption will be considered.
The sanitary towel shortage has led to an increase in infections
The economic crisis has led to a desperate shortage of tampons and pads and many women cannot afford them.
Trade unionists say the government initially agreed to waive duty charges.
"We will pay because women can't wait, but we want the government to reimburse us," Thabitha Khumalo of the Zimbabwe Congress of Trades Unions told the BBC.
The first 40-ton truckload of what is hoped will be monthly shipments is due to leave South Africa in the next few days.
With an 80% unemployment rate and a minimum monthly wage of $21, a packet of 10 sanitary towels costing $5 is beyond the reach of most Zimbabwean women.
The government maintains the problem is being blown out of proportion.
The ZCTU launched the sanitary towel appeal in October last year in the UK and South Africa and has been overwhelmed with the response from big business as well as ordinary South Africans.
Zimbabwe's deputy information minister said the involvement of the ZCTU - allied to the opposition Movement for Democratic Change party - had politicised the issue.
"People are creating a crisis that does not exit. It's a lie to seek attention," Bright Matonga told the BBC's Focus on Africa programme.
The ZCTU says that the ministry of finance had promised in February that duty charges would not be applied and has reneged because the trade union is not a charity.
"It's a dignity issue. I don't see why we should pay duty. Over and above that, every single woman will benefit because it's a free distribution," Ms Khumalo said.
But Mr Matonga said the organisation should apply to the health ministry for duty exemption and a quality-control test, after this the sanitary ware could be distributed by the ministry.
The move has been criticised by international organisations involved in raising money.
"These are donated goods, not a political issue. It's outrageous to make gain out of international solidarity between women," Action for Southern Africa's Euan Wilmshurst told the BBC News website.
Congress of South African Trade Unions' Peter Craven said it was "absolutely deplorable".
Until 1999, sanitary towels were manufactured locally but the economic crisis has meant many companies have left Zimbabwe.
A truckload of donated sanitary towels are waiting to be shipped
Ms Khumalo says the critical shortage has been ignored as it is taboo to talk about periods in public, which is why the unions sought international help.
"Women have resorted to using newspapers, tissue papers and those in rural areas are using leaves and the bark of trees," she said.
This, she says, has led to an increase of vaginal infections.
"Gone are the days when women were embarrassed to talk about it because women are getting sick."
Mr Matonga dismissed these allegations saying there were enough sanitary towels available.
"The Zimbabwe government won't sit back and let women suffer. We care about our women," he said.
The ZCTU said it will raise the money for the duty from its partners abroad and hopes to be able to start distributing sanitary towels to women next week.