"We are not responsible for those policies and we play no part in their development," Smith-Gander said.
Immigration is a sensitive issue in Australia and two years ago the government re-introduced a policy of intercepting refugee boats and processing applications for visas on Nauru and Papua New Guinea.
The programme has come under renewed criticism since a Somali woman said she was raped in custody on Nauru.
Chief executive Grame Hunt said the company had "zero tolerance" of mistreatment and rejected any suggestion Transfield staff were involved in abuse.
The company is about to finish a contract worth A$1.2 billion for 20 months, and is hoping to renew it for five years for an expected income of A$2.7 billion.
Among several rights activists to speak at the meeting, Mohammad Ali Baqiri from Afghanistan told how, as a boy held on Nauru for three years from 2001, he regularly saw prisoners attempt suicide.
"Detention centres are worse than prison," Baquiri said.
"At least in prison you know you`ve committed a crime ... it`s ethically and morally wrong to profit from abuse."
Other activists suggested Transfield`s share price was being hurt by the programme.
"Things are not going well for your company and they`re going to get worse," a woman told the meeting before security staff removed her.
A year ago, Transfield rejected a takeover approach from Spain`s Ferrovial SA at A$2 per share. The stock is now barely half that, having seen several large shareholders exit citing rights concerns.
The United Nations has said an increase in rapes was being reported and it was concerned about a lack of response from Nauru police.
"Impunity for such serious crimes increases the risk they will be repeated," UN human rights spokesman Rupert Colville said on Tuesday.
Australia`s policy has attracted interest from conservatives in Europe where large numbers of people are seeking refuge from war in the Middle East.
Former prime minister Tony Abbott on Tuesday urged Europe to close its borders, telling British conservatives an instinct to help "is leading much of Europe into catastrophic error".
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