The United States has filed a complaint at the World Trade Organization challenging Indonesia's rules for imports of horticultural products, animal products and animals, the WTO said on Thursday.
The complaint says Indonesia's non-automatic import licenses and quotas "have significant trade-restrictive effects on imports and are used to implement what appear to be WTO-inconsistent measures", a WTO statement said.
Details of the complaint, which could lead to a request for arbitration if not settled within 60 days, were not immediately available and are likely to be published within the next few days.
The dispute, the first to be filed at the WTO in 2013, follows repeated questions about Indonesia's policies from the United States, Japan, the European Union and Canada in WTO committees.
Indonesia's Trade Minister Gita Wirjawan said the government was "preparing materials" and will communicate directly with U.S. government officials about the matter.
"We will prepare all the needed steps to resolve these problems," he said in Jakarta.
Indonesia, which has fielded a candidate to be the next head of the WTO, has also upset some trading partners and some of its own citizens with a plan to become self-sufficient in food commodities and which involves cutting back on imports.
Southeast Asia's largest economy suffered trade deficits for four straight months last year, from April to July, and racked up a record monthly deficit in October.
Agriculture contributes around 15 percent to the GDP of Indonesia, employing about 42 million people of a population of roughly 240 million.
Late last year, the OECD grouping of the world's top economies urged Indonesia to reform export taxes and import curbs on farm commodities.
Soon after, President Susilo Bambang Yudhoyono signed a new food law that puts domestic output and demand, and the control of imports and exports, at the heart of self-sufficiency efforts.
Indonesia is also separately being challenged by Australia, Turkey and Sri Lanka to explain its decision to slap a 20 percent emergency tariff on wheat flour after an appeal from Indonesian mills who said imports were hurting their business.
(Additional reporting by Yayat Supriatna in JAKARTA; Reporting by Tom Miles; Editing by Miral Fahmy)