"EU's action of banning vegetables and mangoes in our view is pre-mature and it shocked us...," Commerce Secretary Rajeev Kher said here.
He said that EU's agency on sanitary and phyto-sanitary, and India's National Plant Protection Organisation and Agricultural and Processed Food Products Export Development Authority (APEDA) were already discussing the quality issues.
Concerned agencies from both the sides had reached at an understanding and India had already initiated the process to put in place the proper mechanism to deal with the matter related with exports of vegetables and mangoes from India to EU, he told reporters.
"For all exports, we have specified a procedure which would necessarily have to involve pack-home before the shipments are made and in our estimation that would have taken care of the problem," he added.
Kher said that India has urged the EU's director general for trade to arrive at an early solution for the issue.
Commerce Minister Anand Sharma has already wrote a letter to EU Trade Commissioner Karl De Gucht on the matter saying that the ban has caused considerable apprehensions and alarm in the country.
"It is surprising that the EU Commission has chosen to take this unilateral action without any meaningful official consultation," Sharma's letter has said.
It has said that India has mandated strong (SPS) sanitary and phyto-sanitary (related with plants and animals) standards and those norms are enforced by state-run regulatory body, which ensures appropriate compliance.
The EU's decision is "unfair" and it would potentially jeopardise India-EU agri trade.
On Monday, the EU banned the import of Alphonso mangoes, the king of fruits, and four vegetables from India for the period from May 1 to December 2015 after authorities found consignments infested with fruit flies.
The ban was imposed on Alphonso mangoes, eggplants, the taro plant, bitter gourd and snake gourd to tackle "significant shortcomings in the phytosanitary certification system of such products exported to the EU."
Imports have been restricted as 207 consignments of mangoes and some vegetables shipped from India in 2013 were found to be contaminated by pests.
The UK imports almost 160 lakh mangoes from India and the market for this fruit is worth almost 6 million pounds a year.
India, the world's largest mango exporter, sells about 65,000-70,000 tonnes of all varieties of the fruit overseas out of its total production of 15-16 lakh tonnes.