Some 10,700 companies responded to last month's survey by the private credit research firm Teikoku Databank.
78 percent of the respondents said partnerships and buyouts of Japanese companies by Chinese and Indian businesses would threaten Japan's economy.
The reasons they gave include a technology drain that would compromise Japan's international competitiveness, and more companies moving their production bases overseas.
Companies from emerging countries have been rushing to buy highly skilled Japanese firms in recent years.
In 2006, a Chinese solar cell maker bought a Japanese rival, MSK, and in 2010, a Chinese carmaker purchased a factory owned by Japanese metalworks company Ogihara.
Teikoku Databank says Japanese companies should not feel threatened by emerging economies but establish business strategies to tighten cooperation with those nations.
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