It has also permitted imports from land port and airport in Delhi besides land borders.
The move could help in increasing availability of the fruit in the domestic market and ease its prices.
Last year in September, the government had restricted import of apple by allowing its inbound shipment only through Nhava Sheva port in Maharashtra.
Import of apples "is allowed through sea ports and airports in Kolkata, Chennai, Mumbai and Cochin; and land port and airport in Delhi. Import of apples is also allowed through India's land borders," the Directorate General of Foreign Trade (DGFT) has said in a notification.
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Apple is the most heavily consumed imported fruit in India. India is world's third-largest producer of apples. Depreciation in the rupee, which is hovering at around 66 against the dollar, makes imports costlier.
Apple production in the country is limited to the hilly states of Jammu and Kashmir, Himachal Pradesh and Uttarakhand.
India imports the fruit from the US, China, Chile, New Zealand, Italy, Iran and Afghanistan, among others.
During April-September 2015, India's apple imports stood at USD 153.6 million. The domestic production is estimated to have declined to 18.85 lakh tonnes in 2014-15 as against 24.98 lakh tonnes in the previous year.