A satellite mission goes through different phases: planning, building, launch, operation.

I was wondering what percentage of the whole cost is consumed by the operation and maintenance of a satellite that is already in orbit. Let's say for a small satellite (like a cubesat) for scientific purpose? Someone has to maintain a receiving ground station, check the satellites health systems and so on.

Are there any sources or publicly available analyses on the topic?

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    $\begingroup$ I don't think there is any way to meaningfully answer your question, it is way too broad. What do you mean with "small satellite", in relation to its function? My guess would be that some of the cheapest were "Beer Can Satellites" from 60's that were added to some launchers for ballast, and likely only cost as much as their retrieval on reentry did. Or OSCAR satellites. Nowadays, PhoneSAT likely don't cost much to operate, if at all anything. $\endgroup$ – TildalWave Nov 22 '13 at 0:06

A satellite itself which is on an orbit high enough to not interact with the atmosphere is essentially maintainance-free. Without atmospheric drag it won't need any course corrections to maintain its orbit. It just stays there indefinitely.

Now about it's operation: This really depends on what the satellite is doing. Do the instruments need regular instructions from earth? How difficult is it to come up with these instructions? Does it send signals back to earth? How much effort is needed for analyzing its transmissions? How strong is its transmission power and how much data does it transmit? Is it OK when it can only be reached from time or does it need constant contact to a ground station? When the latter, do its orbital characteristics allow to use existing ground stations or will it be necessary to build and maintain new ones? Are we talking about one satellite or a satellite system consisting of multiple ones (in that case you could likely reduce cost-per-satellite significantly through synergy effects)?

Depending on these factors, the cost can vary between zero and several million per year.

One random figure I could find: The European Galileo and EGNOS navigation systems together are estimated to cost 800 million Euro in maintainance per year after completion. These systems consist of 48 satellites. Does that mean one satellite of the system would cost 16.7 million per year? Unlikely, because you would need almost the same number of operators and ground equipment. Would it be possible to do it cheaper when it wouldn't be an EU government project hampered by countless political factors? Likely.

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