In contrast to the pessimism of Japanese investors in China, China's investment in Japan rose 100 percent year-on-year in the first half, even as China's overall outward direct investment slid 5 percent, said the ministry.

Bilateral trade expanded 3.2 percent in June, compared with 0.4 percent in May.

Infographics: Ties that bind China-Japan trade

Investment from Japan ebbs amid uncertainty

In the first half of this year, China's overall FDI inflows increased 2.2 percent to $63.33 billion, with the June inflow edging up just 0.2 percent to $14.42 billion, said the ministry.

Shen Danyang, a spokesman for the Ministry of Commerce, said that foreign companies in China will continue to enjoy "great opportunities" and FDI inflows will maintain steady growth throughout 2014.

"In the near future, China's FDI inflow will probably enter a new phase marked by restructuring and slow growth. Foreign investment centering on the Chinese market offers bright prospects following the opening of the service sector, although foreign investment oriented toward exports and manufacturing will further decline," Shen said.

He added that China's ODI will increase about 10 percent this year.

Ministry upbeat on export growth picture

China's export growth should show marked improvement in the second half of the year compared with the first six months, the Ministry of Commerce said on Tuesday.

Shen Danyang, spokesman for the ministry, said China is likely to achieve its 7.5 percent growth target for trade if it puts in some effort.

China's trade performance improved in June but still missed market forecasts, reinforcing expectations that Beijing will have to unveil more stimulus measures.