The blue-chip NSE Nifty 50 index fell 0.26% to 15,680 at close and the benchmark S&P BSE Sensex was down 0.31% at 52,318.60. Both indexes gained about 1% in June, helped by declining COVID-19 cases and a surge in vaccinations.

India's factory activity contracted for the first time in almost a year in June as restrictions to contain the deadly second wave of the coronavirus triggered declines in demand and output that pushed firms to cut more jobs, a private survey showed on Thursday.

Meanwhile, the Indian rupee weakened to its lowest level since late-April in afternoon trade on Thursday, hurt by a broad dollar strength ahead of the U.S. jobs data and weak domestic shares.

The Nifty IT index and Nifty energy index were top drags among other sub-indexes, falling 0.57% each.

The Nifty Auto index and Nifty Pharma Index, however, kept sentiment slightly upbeat with gains of 0.82% and 0.93%, respectively. The Nifty pharma index posted its fourth session of gains in five.

Tata Motors Ltd and Bajaj Auto Ltd were among the top boosts on the Nifty 50, adding more than 1% each after both posted higher sales for June compared with a year earlier.

Among losers, drugmaker Zydus Cadila closed 0.9% lower. The company said it was seeking approval of India's drug regulator for emergency use of its COVID-19 vaccine, which showed a 66.6% efficacy against positive cases in an interim analysis.

Vegetable oil refiners such as Ruchi Soya and Natraj Proteins fell between 1.9% and 4.1%, after the government removed restrictions on imports of refined palm oil and lowered its import tax.

(Reporting by Rama Venkat in Bengaluru; Editing by Krishna Chandra Eluri)