The WHO had said in October that the four syrups, made by India's Maiden Pharmaceuticals, may be linked to the deaths of at least 66 children.
But India's drug regulator said in a letter that the WHO has not provided any evidence yet.
India is a major supplier of generic drugs to Africa.
The letter, dated 13 December, was written by Dr VG Somani, India's drugs controller general, and addressed to Rogerio Gaspar, director of regulation and prequalification at the WHO.
India had said in October that it was investigating the cough syrups after the WHO issued an alert.
The WHO said it had tested samples of the syrups - Promethazine Oral Solution, Kofexmalin Baby Cough Syrup, Makoff Baby Cough Syrup and Magrip N Cold Syrup - and found that they contained "unacceptable amounts of diethylene glycol and ethylene glycol as contaminants"
Diethylene glycol and ethylene glycol are toxic to humans and could be fatal if consumed.
But in his letter, Dr Somani said that the samples it tested at a government laboratory "were found not to have been contaminated" with the compounds. The junior minister for chemicals and fertilisers, Bhagwanth Khuba, also told Parliament this week that the cough syrup samples "were declared to be of standard quality" by a government analyst at the Regional Drug Testing Laboratory in Chandigarh.
The test results are being further examined by a panel of Indian experts.
Dr Somani added that the panel had also requested "specific information" from the WHO on "further details essential to establish the causality" but had not received this yet. The letter did not specify what information the committee had asked for.
When contacted, Dr Somani's office asked the BBC to get in touch with India's health ministry. The BBC has emailed the ministry and the WHO for comment.
A senior adviser to India's information and broadcasting ministry told the BBC that the WHO had been "presumptuous" in blaming the cough syrups for the deaths of the children.
"Subsequent inspections, tests and studies by Government of India's notified bodies and technical team have shown that WHO's presumptuous statement was untrue and incorrect," said Kanchan Gupta, adding that the WHO had "[jumped] the gun without valid scientific reasons".
The WHO's intervention came after medical authorities in The Gambia detected an increase in cases of acute kidney injury among children under the age of five in late July. The government later said around 69 children had died from these injuries.
But a representative of The Gambia's national regulator said in late October that it had not yet confirmed whether the medicines were responsible for the deaths.
"We haven't concluded yet it is the medicine that caused it. A good number of kids died without taking any medications," Tijan Fallow said, according to Reuters. — BBC
