Train speed limits are set by the railroad. They declare a piece of track to be of a certain class. Excepted, Class 1 up through I believe Class 7, each class has a MAS. Excepted, for example is 10 with no passenger traffic and a limit on consecutive hazmats. Class 1 is 10 Freight/15 passenger. Class 2 is 25MAS for freight. Anyway, the railroad sets the track class and has to maintain it to said class, if the maintenance falls behind, there are two options. 1: Drop the class of track to bring the MAS down to the track's capability. This is a more permanent move. 2: Put a temporary speed restriction in place and have it on each day's bulletin order for speed summaries, this involves a little more paperwork each day but generally implies they plan on upping the speeds again. Anything less than 10 is likely a specific obstacle as its not a common MAS. Derailment sights and old bridges are common causes of these.
Anyway, rambling on. The FRA comes in and tests the track. If the track fails to meet the criteria of the tracks class, they place a speed restriction. So really, the FRA can only enforce track standards and corresponding MAS, but they do not set the timetable MAS for a given stretch of line.
Hope that answers your question thoroughly.