Are healthcare organization changes controlled by the fedeal and state governments?

Actually, "health care organization changes" is an unclear term, there
are laws and recommendations like HIPAA an others that need to be
satisfied, if you are in US and want to make changes to a regd health
care organisation, you should be knowing abt HIPAA (Health information
preventability and accountability act) and IRB (Instructional review
board). Other recommendations can be made by JCAHO, Leapfrog group and
some other organizations which are very reputed.
This is a good place to see all government agencies at one place and what they do:

http://www.fealth.com/gov/governmenthealth.html

Hope this helps!

Some healthcare organization changes are made in reponse to
Medicare/Medicaid funding changes (either on the Federal level or the
state level, or both) ;
some are made in response to fereral HIPPAA regulations (around
privacy of records, billing information, health information).

What is the specific change you are looking at ?

You can probably get an answer by calling the office of your State
Representative or Senator - in my experience they have crack research
teams who are very responsive to voter's issues.