The matter came up during a meeting here between Commerce and Industry Minister Anand Sharma and US Food and Drug Administration (USFDA) Commissioner Margaret A Hamburg.
"We are going to give a non-paper (to the US) overall on some of our concerns, when it comes to duration for the registration process for the filing," Sharma told reporters after the meeting.
Hamburg said the meeting was "excellent" and didn't comment further.
An official said India drew the Commissioner's attention to the fact that most of the time, audit inspections were not followed by discussions with companies. In some cases, clarifications were sought but even before a response, harsh decisions were taken.
"Attention was also drawn to disproportionate penalties imposed by USFDA on some companies," the official added.
The non-paper would highlight India's concerns with a view to seek an early resolution on these issues.
The USFDA has taken a series of actions against Indian pharmaceutical firms, restricting their shipments to the US, their largest export market.
The US health regulator on January 23 banned the import of products manufactured by Ranbaxy Laboratories at its plant at Toansa. This was the company's fourth plant to face regulatory action from the USFDA, after Mohali, Paonta Sahib and Dewas plants.
In 2013, Ranbaxy had agreed to pay a fine of USD 500 million to US authorities after pleading guilty to 'felony charges' relating to manufacture and distribution of certain adulterated drugs made at the Paonta Sahib and Dewas units.
Another Indian firm, Wockhardt, had its two plants put under import alert by the USFDA.
According to sources, such steps by the USFDA would affect India's pharma exports to the US.
India's pharma exports increased 10 per cent to USD 14.6 billion during 2012-13, with shipments to the US accounting for about 26 per cent of the total.
India is the largest exporter of generics to the US by volume, with supplies from 35 companies in the country. The nation has around 320 USFDA-approved pharma facilities, the largest number outside the US.
India also raised concerns over the high fees for certain services rendered by the USFDA and delays caused in several approval processes.
Sharma said pharmaceutical issues were discussed "very clearly" as was cooperation in the sector.
"These issues do come up before the countries. What is important is the willingness to address those issues and resolve matters, which we have definitely mentioned," the minister said.
He said India is a major exporter of pharmaceuticals to the US.
After US companies, the second-highest number of FDA approvals are with Indian pharmaceutical companies, he added.
Both sides agreed that the pharmaceutical industry should be educated about certification and registration processes.
The minister also proposed an institutional framework and linkages with the agriculture sector, especially with the Agricultural and Processed Food Products Export Development Authority, the Marine Products Export Development Authority, the National Plant Protection Organization of India and the Spice Board of India.
India is a major exporter of spices and marine products to the US.
"I do hope that what we have agreed to will create a structure of regular exchange," he said.
The two officials also discussed acceptable levels of pesticides in Indian agricultural products such as rice and pomegranates.
India told the Commissioner Hamburg that pesticide level norms should be based on actual health risk.
India has been seeking market access for the export of litchis to the US. The matter is stuck with the US Environmental Protection Agency, which has raised the issue of chemical residues.