He told Westminster's transport committee that Maritime and Coastguard Agency (MCA) operations were part of a national organisation, and the government had not looked into breaking it up and had no intention of doing so.
The Scottish Government is currently seeking views on whether coastguard services should be devolved, following anger over plans to reduce the number of MCA centres in Scotland from five to two.
Mr Penning was responding to a question from Conservative MP Iain Stewart.
"This is a national emergency service and the government have not looked at, and have no intention of looking at, breaking that up under the devolution settlement," Mr Penning said.
"The coastguard is seen as a national organisation and will go forward as one."
Mr Penning said there was a risk of "fragmentation" and reduction in quality if the service was broken up.
The committee has been holding hearings over the government's proposals to reduce the number of maritime rescue co-ordination centres.
Under the plans, Aberdeen would be the only Scottish coastguard station to be spared from the cuts, while a second station would operate only during daylight hours - either at Shetland or Stornoway.
An evidence-gathering meeting of the committee was held in Stornoway last week.
Mr Stewart said he had asked during that session if there were any logistical or practical reasons why the service should not be devolved, and the coastguards had said there were not.