While I don't hold the classic conspiracy theories with much regard, I wouldn't be at all surprised if governments - and those that can influence them - have likely covered up the true details of many events. I don't believe what they are hiding is necessary maliciousness, instead they hide their failings and shift blame that should fall on them elsewhere.
Here in the UK, the obvious example is Hillsborough (which is currently back in the news as several people have finally been charged with crimes relating to the disaster). Neither the Thatcher government, nor South Yorkshire Police, nor those involved in the design and operation of the football ground tried to kill the 96, but once it had happened, instead of taking responsibility for the negligence that had allowed it, they, with the help of parts of the media, instead blamed the very people caught in the fatal crush. It's taken the best part of 30 years for the truth about what happened to fully emerge.
I fully expect many other such cases exist - failings on behalf of the authorities that they have hidden and blamed others for.