Final report rejected, institution asked to return funding and prosecute my supervisor When I finished my PhD, I was working on a small grant project worth €6000 with the aim of integrating computational software and public services offered by another institution. In our final report, I stated why we did not achieve one of the objectives (due to technical complexity discovered during the project beyond the project scope: the technical complexity might be known by experts; however, we were not experts at the time of writing the grant proposal).

The other objectives were met; the grant report was finalized and left to my supervisor, who was the coordinator of the project. 

Due to several circumstances, the project was evaluated after 2 years. It was rejected, as the funding was not met in part of university participation, the reviewers rejected also the project due to not fulfilling some of the objectives. 

It seems that supervisor will be liable and need to return the funding, or it will be deducted from his salary.

Am I morally liable to participate in this return, even though no fraud or misconduct was done?
You are absolutely not responsible for returning any funding, certainly not at a moral level and almost surely not legally either.  You were engaged in research to the best of your ability; as you were not the person who obtained and was responsible for the funding, you are not responsible to the funder for any failures.

Moreover, I think it is pretty unlikely that the funding body will actually claw back any money from your former supervisor.  Unless there was genuine skullduggery and/or intent to misuse the funds, the worst that is likely to happen is that the supervisor will be required to resubmit a much better explanatory report.