M Rajeevan, Secretary of the Ministry of Earth Sciences, said, "monsoon was 95 per cent of the Long Period Average (LPA), which is below normal".
Anything between 96 to 104 per cent of the LPA is considered as a "normal" monsoon.
The India Meteorological Department (IMD) had revised the monsoon forecast to 98 per cent of the LPA in June after earlier pegging it at 96 per cent.
"The first two months of the monsoon season witnessed 3 per cent more rainfall above normal, while the remaining two months witnessed deficiency of 12.5 per cent," said M Rajeevan.
The rainfall season in India starts from June 1 and ends on September 30.
Of the 36 weather subdivisions of the country, six -- East Uttar Pradesh, West Uttar Pradesh, Vidarbha, Punjab, the cluster of Chandigarh, Delhi and Haryana and East Madhya Pradesh -- received "deficient" rainfall.
M Rajeevan said the southern peninsula, the east and the northeast regions received good rainfall.
The season also witnessed several parts of the country such as coastal Maharashtra, including Mumbai, Gujarat and Rajasthan and the northeastern states, being battered by extremely heavy rainfall.
The monsoon was not that bad and there was also no reason to expect drought in parts of the country, M Rajeevan said.
"There could be some impact on agriculture in some parts of the country, but the Agriculture Ministry is in a better position to talk on this," he added.
Several parts of the country are witnessing agriculture distress.
Earlier this year, there were reports that an El Nino, a phenomenon associated with the heating of Pacific waters, could impact the monsoon.
But the IMD had downplayed it and later revised the monsoon forecast to 98 per cent of the LPA.
It had also said that there were prospects of a positive, but weak India Ocean Dipole (IOD). The IOD is associated with the heating of the waters of the Indian Ocean and a positive IOD can have a good influence on the monsoon.
"We had said that the monsoon could be 98 per cent of the LPA with an error margin of five per cent. So, that is well within our forecast," M Rajeevan said.
He attributed the slack in the rainfall in August and September to the typhoons over the Pacific Ocean and a negative IOD due to warming of the east Indian Ocean waters.
"We don't know the exact reason behind the low rainfall in the last two months of the season. Our scientists are studying the reasons behind this," he said.
The Southwest monsoon's onset over Kerala was on May 30, two days before its normal arrival date while it started withdrawing on September 27, 12 days after its normal withdrawal date.
In the last four years, three rainfall seasons have been below normal. Below normal rainfall was registered in 2014, 2015 and 2017 while 2016 recorded normal rainfall.