Loss of confirmed orders, increase in wages and labour shortage were blamed on the scheme in a survey of 100 companies from diverse sectors.
The industry has called for the inclusion of industrial labour under the Mahatma Gandhi National Rural Employment Guarantee Act in areas with heavy industrial activity.
The demand assumes significance in the wake of agriculture minister Sharad Pawar's recent statement in Pune the scheme would be used to provide farm labour.
Responses to the survey, titled 'Labour Shortage for Industry', by Ficci said many companies faced losses due to labour shortage.
Nearly two thirds of participating firms said potential losses due to labour shortage caused by MGNREGA were to the extent of 10
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