As many as 159 cases of Zika were reported in Jaipur during October-November.
The government has urged the US to "withdraw or modify" its advisory against travelling in India, which was issued after Zika cases were reported in Rajasthan and Madhya Pradesh, saying the outbreak has subsided.
The US government's Centers for Disease Control and Prevention last month advised pregnant women against travelling to areas with risk of Zika in India.
Raising concern over the advisory, Director General of Indian Council of Medical Research (ICMR), Dr Balram Bhargava, said it has created an impression that the outbreak of the disease is still continuing.
"I wish to bring to your attention that Zika virus outbreak in both Rajasthan and Madhya Pradesh have now subsided completely. There are no reports of fresh cases and vector indices are also well within acceptable limits.
"I urge you to take up the matter with the concerned authorities at CDC and withdraw/modify the travel advisory," Dr Bhargava said in the letter.
In a note attached to the letter, Dr Bhargava mentioned that multiple human and vector samples tested from affected areas confirm the absence of any active transmission of Zika virus.
The CDC in its advisory stated that Zika is endemic (regularly found) in India and an outbreak of the disease has been reported in Rajasthan and surrounding states.
"Pregnant women should not travel to areas with risk of Zika. A pregnant woman can pass Zika virus to her fetus and infection during pregnancy can cause serious birth defects," the advisory read.
However, one who has to travel was advised to talk to doctor or other healthcare provider before undertaking the journey and strictly follow steps to prevent mosquito bites during travel and for three weeks after his or her return.
It said one should strictly follow steps to prevent sexual transmission during the trip and see doctor after return, even if there are no symptoms. "Tell your doctor about possible Zika exposure at each prenatal care visit."
As many as 159 cases of Zika were reported in Jaipur during October-November. In Madhya Pradesh, 130 cases were reported during the same period, whereas in Ahmedabad the number of cases were two.