O problema não parece estar no lado do PostgreSQL, então você provavelmente deve procurar a ferramenta de conversão para o bug. Do psql:
test=# CREATE TABLE import (id int NOT NULL PRIMARY KEY, val1 int, val2 int);
NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index "import_pkey" for table "import"
CREATE TABLE
test=# COPY import FROM STDIN (FORMAT CSV);
Enter data to be copied followed by a newline.
End with a backslash and a period on a line by itself.
>> 1,,111
>> 2,22,222
>> \.
test=# SELECT * FROM import;
id | val1 | val2
----+------+------
1 | | 111
2 | 22 | 222
(2 rows)
