I am assuming you are refering to an instruction which results in a compensation event, most of which will be to change the Works Information. If not, please correct me.
Off the top of my head, I cannot think of a single contractual exception whereby if the Project Manager instructs, the Contractor has to do. Indeed, if the Contractor delays doing whatever is instructed and this results in higher costs, then the assessment of the compensation event would be reduced under clause 63.7 as the Contractor has not reacted promptly to the compensation event.
In short it depends on the main option and nature of the PMI.
If the PMI is a change to the Works Info, the PMI needs to be undertaken by the Contractor and this is separate from the assessment of a compensation event. With the timetables within NEC3 it is most likely that the works will be underway before your CE quotation has been agreed. NB Not all PMIs are CEs so you are not guaranteed to be paid extra costs on all PMIs.
Its worth noting that payment mechanism under the main option (for example option B, C, E, etc) also changes the answer (to what you get paid rather than costs agreed) in certain circumstances.
Just to clarify the last answer. In instances, whereby the contractor has reacted promptly and seeks clarification to an instruction issued as not a CE. Should the contractor continue without agreement to costs? Also, if the contractor has met the WI for meeting a key date, and then the above occurs, what then?