This may be your first industry project for which you require questionnaire, but for the employees they may have came across enormous project trainees and questionnaire.
First be confident and learn the pattern of people there. It's not all the 100% people are behaving in the same reluctant manner. Approach soft-people first. Before directly handling them your questionnaire, discuss the importance and the outcome of such projects with them while at lunch and break. Your questionnaire should reflect the help you want not a huge task for them. (May be due to this someone shouted at you) Prepare a list of the people, divide them into groups and select accordingly.
Once some people filled the questionnaire, encourage them to persuade their fellow members too. It should feel like a task to them but their good sharing.
Most importantly first built a small bonding with them. Why the people would favor you and share their thoughts before having a good thoughts-link with them?
It's not you will take the help of HRD only, take help of yourself. If possible, scan your questionnaire again; think from the perspective of an employee, not employer. (No. of sample, target people, no. of questions, subjective-objective questions ration, etc).
Don’t worry; all come across through such problems. Please feel independent, involve HR but to a certain limit. Don’t approach people when it’s their high working hours. Be humble.
You can also complete your Questionnaire through verbal interaction with people and later recording it in paper for some people.
My best wishes.