Prof Thomas Bley has been a design lecturer at the university for five years, and had been working hard to create an internationally recognised school of design.
"The bottom line is, I had hoped to set up something internationally competitive. It seems I won't be able to do that now."
Prof Bley believed many of his colleagues in the department shared his frustration at the lack of opportunity to create a globally-recognised programme.
Before arriving at the university, he founded the International Design Network and Institute (iDNI) and was a partner in Spider AG.
He has also been president of Zebra Design in New York, general manager of Frogdesign, and was a member of Memphis - the most influential design group of the 1980s.
Parallel to his professional career, Prof Bley held academic positions at Parsons School of Design in New York, Arizona State University, Glasgow School of Art, University of the Arts in Philadelphia, California College of the Arts in San Francisco and, most notably, he was co-founder and Dean of the School of Design at the University of Applied Sciences in Cologne.
Reflecting the international and cross-cultural importance of design, Prof Bley founded the Master of European Design programme, where students were able to take advantage of the diversity of programmes at seven leading European universities in Helsinki, Stockholm, Glasgow, Cologne, Stuttgart, Paris and Milan.
He had hoped to create a course with similar stature at the University of Otago.
The proposed merger was announced on Thursday morning by pro vice-chancellor, sciences, Prof Vernon Squire.
Yesterday, Prof Squire told the Otago Daily Times the university was facing a difficult financial environment and the proposal was partly the result of this situation.
Prof Bley said the merger was aimed at saving the university money on administration costs, and was critical of the proposal.
"This may save them some money. But in the end, if they don't deliver a world-class programme that will attract the students, they won't make money."
Prof Squire said the proposal aimed to advance the university's dedication to using science and improving research quality and productivity.
The new department of Applied Sciences would be a focus for a remodeled and more flexible version of the bachelor of applied science (BAppSc) and bachelor of consumer and applied sciences (BCApSc) degrees.
Students enrolled in courses in the departments at present would be able to complete their qualifications as they had planned, he said.
The proposal has left about 30 academic and administration staff puzzled about their future, but Prof Squire said it was too early to say if jobs would be lost in the restructuring.
"It is too early to determine how this might affect jobs and a specific time-frame is not established."