I had this with a 03 Civic 1.7 CDTi, The Honda dealer in stirling use every Diagnostic kit they had and nothing showed up.
They got the "old" mechanic to look at it (he didnt like using the diagnostic computer) He found that the Fuel Filter (the little one just before the High pressure pump) was clogged up with a load of junk. The Engine managment System recognised the shortage in fuel and just limited the engine. Cost £220 to get the Fuel system cleaned and have all the filters replaced, car was under warrenty at the time but this kinda thing is not covered.
Turns out the <
INSERT EXPLITIVE HERE> Garage in cambridge that did my 72000 mile service didnt replace the fuel filter but charged me for it

(Only thing they did do was change the Oil)