 In 1849 he had a dangerous illness but recovered, and in 1852 was appointed to administer the diocese during the absence of Bishop Broughton on a visit to England.The bishop died in February 1853 and Cowper had to continue his duties until Bishop Barker arrived in May 1855.The new church of St Philip was sufficiently complete to be consecrated in March 1856, much to Cowper's joy.