There are two possible channels for industry to influence economic evaluations. The first is when industry players are the research funders (e.g. funding the research or they themselves conduct it). The second is that they are providing information or advice on methodological approaches to be used in economic evaluations conducted by independent bodies.
The first channel can be prevented through a legal process of independent bodies to review industry submissions. This is a well-established process in Australia (
http://www.pbs.gov.au/info/reviews/pbac-guidelines-review). For some countries, this is avoided through non-inclusion of industry submissions in the policy process (currently, the Thai system on development of pharmaceutical reimbursement follows this approach, although it used to allow industry submissions in the past).
I understand that this question focuses on the second channel and I agree with Lorna's comment that countries need to establish methodological guidelines that clearly specify preferable methods and type&source of information to be used in the study. If the methodological guidelines are good enough, it can prevent many possible biases that may be introduced by researchers and stakeholders, including industry. This is why the GEAR online resource underlines the importance of guidelines. If countries don't have guidelines, as you may see that the GEAR shows many countries without guidelines, I would recommend that they follow internationally available guidelines, such as the reference case (
http://www.idsihealth.org/knowledge_base/the-reference-case-for-economic-evaluation/).
Lastly, involving many groups of stakeholders (industry, health professionals, policymakers, etc.) that have various and potentially competing interests that would serve as a check and balance on the system. In Thailand, we recommend that stakeholder consultation meetings are conducted before the study starts and just after the completion of analysis. The first one ensures that the study will be conducted using the right approach; the second one ensures that the study results are interpreted correctly and the recommendations are supported by the stakeholders.