The western coastal state, along with Bihar and Manipur, does not have a single district which has been declared ODF, officials said.
However, what is striking is that Goa has only two districts while there are 38 districts in Bihar and nine in Manipur.
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As one of the most well-known tourist destinations in the world, officials feel that there is an urgent need to meet the challenge in the state.
To accelerate the process, Iyer had rushed to Goa to find out the reasons and find a solution to make the state free of open defecation as soon as possible.
"Since the state has just two districts, north Goa and the south Goa, it should have been ODF by now. It is such a small state," a top official in the ministry said.
Officials feel that though Goa is one of the smallest states in the country, the rocky terrain and low water levels make it difficult to have proper water supply. Hence in most rural areas, people are forced to defecate in the open.
According to them, ODF has also become an issue in most of the urbanised areas in Goa, especially at places with ongoing construction, due to uncontrolled and illegal leasing out of premises without toilet facilities to migrant labourers and families.
Official documents regarding Swachh Bharat Mission (Rural) on Goa show that SBM coverage is close to 77.84 per cent in North Goa, where as in South Goa it is 73.81 per cent.
Official data shows that overall SBM coverage in the state was 60.59 per cent in 2014, when the mission was launched, the state increased its coverage to 76.22 per cent in 2015-16 fiscal.
But since then, the per cent of coverage has not increased in the state.
The report also shows that though 28,637 toilets were built 2014, with 15.62 per cent households having the facility, but no records of number of new toilets, or ODF panchayats and villages had been notified since then.
Goa Chief Minister Manohar Parrikar had recently told the Centre that by this year Goa will be declared open defecation-free.
"I was told by the Goa CM that the state will be hundred per cent open defecation-free by October 2018. I have no doubt that the state will achieve this goal," Union Housing and Urban Affairs minister Hardeep Singh Puri had told reporters after chairing meetings to review various urban development initiatives in Goa last month.
Other than Goa, Bihar and Manipur, there are other states like Odisha, Jammu and Kashmir, Uttar Pradesh, Puducherry figure low in the ODF list.
Arunachal Pradesh, Chattisgarh, Gujarat, Kerala and Union territories like Chandigarh and Daman and Diu top the list of ODF with close to 100 per cent coverage.
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