"We need to carefully assess whether the proposed merger would lead to higher prices or a reduced choice for farmers," EU Competition Commissioner Magrethe Vestager said in a statement.
The deal -- the biggest in a series of Chinese overseas acquisitions -- would combine Syngenta, a global leader in seeds and crop protection with ChemChina which controls Adama, the largest supplier of generic crop protection products in Europe.
"The transaction would take place in an industry that is already relatively concentrated," the Commission noted.
The Commission probe will run to March 15.
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Syngenta said this week it was confident the deal would go through, having already been cleared in the United States and Japan.
The Commission said initial investigations showed the new company would have "relatively high combined market shares" in several categories, while ChemChina's Adama would be removed as a competitor with Syngenta.
Given the global scope of Syngenta and ChemChina, the Commission said it would cooperate closely with other competition authorities, notably in the United States, Brazil and Canada.
The Commission recalled that it also has an in-depth probe underway into a proposed tie-up between US chemical giants Dow and DuPont, valued at USD 130 billion, with a decision due February 6.
If the Commission, which oversees competition policy in the 28-nation EU, finds fault with a proposed merger, it can reject the deal but more usually it asks the companies to sell parts of the business, or to allow in newcomers so as to minimise the impact on customer choice and price.