The United States had refused to allow any criticism of Israel in the statement.
China's envoy to the UN complained that the final version was "watered down".
The statement, passed unanimously by the 15-nation council, said: "The security council is deeply shocked and distressed by the firing by the Israeli Defense Forces on a United Nations observer post in southern Lebanon on July 25."
After the meeting, Dan Gillerman, Israel's UN ambassador, said the resolution was "a very fair and balanced statement" about what he called "a tragic accident".
Large parts of the original Chinese draft text were taken out in order to get the "presidential statement" passed.
A paragraph which said "the Security Council condemns any deliberate attack against UN personnel" was deleted, along with a phrase which would have called on the UN to be involved in any Israeli inquiry.
The security council called upon Israel "to conduct a comprehensive inquiry into this incident, taking into account any relevant material from United Nations authorities, and to make the results public as soon as possible".
Wang Guangya, China's ambassador to the UN, said the document was the "minimum" that could be expected from the security council.
Wang said: "Any killing of innocent life has to be condemned."
Wang was asked how the negotiations over the statement would influence talks on a resolution regarding Iran's nuclear programme.
Wang said nearly every delegation in the council was frustrated over the US position.
Wang said: "Definitely this frustration will have its negative impact."
Without mentioning the US by name, he said reluctance by one government "definitely will affect smooth cooperation on other issues."