Can government agencies track what sites I'm visiting when using Tor?
Your question is quite hard to answer, because as far as I know the special capabilities of the agencies in this field are yet unknown.
However you can first look into Tor's design document. Section 3.1 states:
A global passive adversary is the most commonly assumed threat when analyzing theoretical anonymity designs. But like all practical low-latency systems, Tor does not protect against such a strong adversary.
So if you assume that the NSA, GCHQ or any other entity can observer world-wide traffic, Tor doesn't protect you here. Furthermore Matthew Edman and Paul Syverson found more weaknesses when an adversary has can look over many autonomous systems (AS). See AS-awareness in Tor path selection (PDF).
On the other side you can ask yourself why NSA or others will target your person. If they have a special 'interest' in your data, it might be easier for them to install some kind of malware onto your system or to break into your apartment and install a keylogger. Usually this can be done without anybody noticing it. It furthermore has the advantage for the adversary that they can be quite sure to get your traffic data. In the case above they need to apply algorithms which might also lead to wrong conclusions.