The Empire clock counts Empire Time Units (ETUs), just like an ordinary clock counts seconds.
There's always the same number of ETUs between updates (the version command shows how many). ETUs automatically stretch or contract to maintain that when updates move around for some reason, say a change of schedule, or unplanned downtime.
Because of the unique nature of Empire governments, (i.e. the decision makers spend most of their time on vacation. Hmmm, not so unique actually), and the fact that ideally the Empire environment will mirror the real world, various heuristics dealing with time have been implemented.
The first is the Bureaucratic Time Unit (BTU) concept which keeps track of the potential for doing work possessed by your government.
The second heuristic, (i.e. hack), is the Elapsed Time Limit (ETL) which limits the amount of time that players may be logged on each day. The ETL is not cumulative and is reset to some particular value, (often two hours, check the version command to be sure), every night at midnight.
The ETL and BTU counts are displayed with each command prompt
as follows:
[##:##] Command :
The first ## is the Elapsed Time today, in minutes. This number starts at 0 every midnight. The second ## is the number of BTUs remaining.