April will always be expensive as that is a very popular time to visit Japan. The cherry blossom season goes from March to May and then 'Golden Week' at the end of April when the whole country is basically on holiday.
Direct flights are going to be about that much but you will find indirect flights a lot cheaper.
Just checking today on flights leaving the first week in April and returning seven days later there are any number of flights from London to Tokyo for £800 to £1,000.
For example, Lufthansa from London to Tokyo with a two hour stopover in Frankfurt £986.
Or Asiana Airlines with a 2 1/2 hour stopover in Seoul, South Korea for £800.
.
Prices are a bit cheaper at the end of April. For example, a direct flight with BA leaving 24th April and returning 1st May is currently £1,228
The same applies with indirect fares as well.
For example, Air China with a 4 hour stopover in Shanghai for £637
Or Cathay Pacific with a 1 1/2 hour stopover in Hong Kong for £862