The observation that BT Cotton sowing area especially in Punjab is regularly on the rise at the cost of wheat and sugarcane mainly due to the longer germination period of this variety of cotton is something that must not going unnoticed on the part of the agriculture managers as this factor would trigger to much extent the food security issue in the country which is already experiencing a critical situation in terms of severe water shortage for agriculture purposes and low yields. The government had introduced BT cotton in 2002 in the country with an aim to achieve 21 million cotton bales by 2015 and increase the yield per hectare to 1,060kgs, however, unfortunately it failed to prepare any plan to avoid its possible negative consequences on other cash crops like wheat and sugarcane. The germination period of Bt Cotton lasts for about ten months against the normal cotton that takes about six months. Though this cotton variety cultivation has encouraged the farmers during the last couple of years, however, this major factor is having a negative impact on other crops particularly wheat and sugarcane as majority of farmers who had previously sowed normal cotton for six months and sowed sugarcane or wheat for the rest of the year are now unable to do so. The long duration of Bt Cotton is damaging crop rotation pattern which could threaten food security. In fact, it is about regulation by relevant departments as without adopting this effective rotational mechanism, farmers can’t grow the staple food at a required scale in the country. It is also a noticeable fact, that in USA and Australia no one can think of growing GM Corn or Cotton without refugia (an area in which organisms can survive through a period of unfavorable conditions, esp. glaciations). But it is a point of high regret that here in Pakistan nobody has bothered to even design it keeping in view the local conditions. Subsequently, unregulated system has resulted in hazards as is the case with India where non-implementation of refugia resulted in pest resistance development in pink bollworms. But at the same time, it does not mean that we should stop Bt Cotton. Simply it means that we have to manage cropping patterns to ensure food security and rationalise the agricultural and economic benefits accordingly. Hence, without regulatory system GM crops can never be properly managed the country. As wheat, cotton and sugarcane are the three major crops being grown in Punjab. They are individually supporting to three important local industries – food, textile and sugar. Any imbalance in cultivation of said crops will create a serious problem for the whole economy and that is what the government is supposed to handle.